[Freesurfer] Fwd: [Neuroimaging] [Nibabel] Discourse category for Surface API discussions

[Satrajit Ghosh]

External Email - Use Caution

fyi

-- Forwarded message -
From: Christopher Markiewicz 
Date: Mon, Aug 9, 2021 at 5:01 PM
Subject: [Neuroimaging] [Nibabel] Discourse category for Surface API
discussions
To: neuroimag...@python.org 


Hi all,

I'm starting to work on the Surface API portion of the Nibabel grant.

I've created a category on the Discourse here:
https://secure-web.cisco.com/1fZyTqmwozZU5Qoa2utEX0kDdW_8B7XIMEFga96aHR-YctDChh-Zx9cN1SO_1ZHs_xdWuUetZM5VK1uRC1XNJBe7RRgeb09fdKqZK7Fuo0tuUTJMBM9IcuCrTnAKvXvP8FOiP-L0VcuCluMnufN4nIwJJpS50EG8jsc8IDz4bpGskjHV6kESUnY9QF89xoapABaPugxAFVyfRw5wyE8ru4jIh8QQf5T3PUc5iZJ_HgutYCfKx_ovrEaWBk0fMvy_tphmUp6jFt46JB17z8AlX2A/https%3A%2F%2Fnipy.discourse.group%2Fc%2Fsurface-api%2F10

And I've started some initial notes here mostly laying out the problem:
https://secure-web.cisco.com/1qQtCe4EJSW0O7Z_CBMnNittP03bU4FYzr1xy2YZOTw_oawdHMw3nJVKmZQBvF8O3rErC-ZpG0VuwIxcIWO0IgTTPnlkKqCPj5oRMRa8qQfwhcw_iEOc_tD1yHlmjQu2Eztu4hU1rdMCmbHxLgddtj27C5RBrLpK2dYBjLhs-3LWhMVuKovrE_19eEDzEFRrFOg0g-EwwmjAjmAExOHABver1Hfbz5nl0ON7KVhr_lTPmWVaA4Z9kmSxljiBBW2W-P4r9ExaW0nrhdMoaMPJsiw/https%3A%2F%2Fnipy.discourse.group%2Ft%2Fpreliminary-notes-on-surface-representations%2F57

The next steps are going to be to identify use cases for people working
with surface data, which will also involve finding people who I may not
know about, so please forward this on to people who might be interested in
joining the discussion.

--
Christopher J. Markiewicz, PhD
Center for Reproducible Neuroscience
Stanford University
___
Neuroimaging mailing list
neuroimag...@python.org
https://secure-web.cisco.com/1Zrv7RS4PEvZfb7azKaQbWoX5ysGPT8TngX38S6Ud5LMDAzUQbi-LHCGEyu5uAkqOIWsAc2hcY6XBFkbW-EFGCls4IPlbROOV2Jc2A6WOxN3Rz4KZldLgQRG5Tsz4Z7w4d2i3ZFMRCgcAHANNG7L0zreQWWOQoDTh6gt9fhVucR3mqazPTyQyrKPH2LZpeZjvKZxWVfRm_g5k3UYYRH4hQEYsANCgiGceZoN4xxyPSZsau5LEIyVOGBUqUd4q95mHUJwpGihwckMraOTlcvWpkw/https%3A%2F%2Fmail.python.org%2Fmailman%2Flistinfo%2Fneuroimaging
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Pre SFN Workshop Nov 2-3, 2018: Hands-on Reproducible Analysis of Neuroimaging Data

[Satrajit Ghosh]

External Email - Use Caution

*Hands-on Reproducible Analysis of Neuroimaging Data*
*A ReproNim Pre-SFN 2018 Training Workshop*
*Register here: https://tinyurl.com/repronim-sfn18
*
Purpose:

An increasing body of evidence point to some issues in reproducibility in
biomedical or life sciences, raising concerns in the scientific community.
ReproNim has developed a curriculum
 that will give the students
the information, tools and practices to perform repeatable and efficient
research and a map of where to find the resources for deeper practical
training.

This training workshop will introduce material on the key aspects of
reproducible brain imaging and will orient attendees using a hands on and
practical experience to conduct neuroimaging analyses, using the next
generation of tools.  By the end of this course, the student will be aware
of training materials and concepts necessary to perform reproducible
research in neuroimaging. The student will be able to reuse these materials
to conduct local workshops and training and be able to customize the
training for their specific scenario.
Prerequisites:

If you are a student, postdoc or researcher in life science who directly
works with neuroimaging data - or wish to work with these data, and you
have some basic computational background, *this training workshop is for
you*. You should have already done either some R, or Python, or Matlab or
Shell scripting, or have used standard neuroimaging tools (SPM, FSL, Afni,
FreeSurfer, etc) and be engaged in a neuroimaging research project. You
should have already completed a neuroimaging analysis or know how to do one.
Modules:Module Reproducibility Basics: Friday Nov. 2. 9am-10:45am.

This module guides through three topics, which are in the heart of
establishing and efficiently using common generic resources: command line
shell, version control systems (for code and data), and distribution
package managers. Gaining additional skills in any of those topics will
help you to not only become more efficient in your day-to-day research
activities, but also would lay foundation in establishing habits to make
your work more reproducible.
Module FAIR Data: Friday Nov. 2. 11am-12:45.

This module provides an overview of strategies for making research outputs
available through the web, with an emphasis on data. It introduces concepts
such persistent identifiers, linked data, the semantic web and the FAIR
principles. It is designed for those with little to no familiarity with
these concepts. More technical discussions can be found in the reference
materials.
Module Data Processing: Friday Nov. 2. 2pm-3:45pm.

This module teaches you to perform reproducible analysis, how to preserve
the information, and how to share data and code with others. We will show
an example framework for reproducible analysis, how to annotate, harmonize,
clean, and version brain imaging data, how to create and maintain
reproducible computational environments for analysis and use dataflow tools
to capture provenance and perform efficient analyses (docker) and other
tools.
Module Statistics: Friday 4pm-5:15pm

The goal of this module is to teach brain imagers about the statistical
aspects of reproducibility.  This module should give you a critical eye on
the current literature and the knowledge to do solid statistical analysis,
understand the limitations of p-values, the notion of power and of positive
predictive values and how to represent evidence for results.
Reproducible publication project - Saturday 9am-12:00

This is an hands on session: small groups will work with the instructors on
the steps to deliver a fully reproducible publication.
Logistics:

*Location*: University of California San Diego (detail of location will be
given by email)
*Dates*: November 02-03, 2018.
*How to register*: *https://tinyurl.com/repronim-sfn18
*
*Costs*:  25$.
*Schedule*:
*Friday November 2nd:*
8:30-9am: Introduction to the course and
participants “setup”
9am-10:45: Reproducibility Basics
10:45-11am : Coffee break
11am-12:45: FAIR data
12:45-2pm : Lunch+coffee
2pm-3:45: Data Processing
3:45-4pm: coffee break
4pm-5:15pm: Statistics for reproducible analyses
*Saturday November 3rd:*
9am-9:30: Questions and answers and feedback session
9:30-12pm:  The Re-executable Micro Publication
Challenge
  During this time, we will propose a small
challenge around producing an entirely re-executable
  neuroimaging analysis from fetching data
to producing statistical results. This will also be a
  time 

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

[Satrajit Ghosh]

hi lea,

in addition you could consider using the bids app for freesurfer:
https://github.com/BIDS-Apps/freesurfer

and then submit each subject's longitudinal pipeline as a separate slurm
job.

cheers,

satra

On Thu, Feb 22, 2018 at 10:43 AM, Martin Reuter  wrote:

> Hi Lea,
>
>
> I wrote that script to simplify processing on our cluster which uses qsub
> PBS for submission. I have never used SLURM so far.
>
>
> There is two functions that you (or someone who knows this stuff) would
> need to modify:
>
> def submit
>
> and
>
> def wait_jobs
>
>
> The submit procedure basically issues a submit command (stored in pbcmd).
> The examples there should help anyone who programs python to modify it for
> a slurm submission.
>
>
> The wait_jobs scripts runs a different command (here qstat and grep user)
> to see how many jobs you are already running and waits until this number
> sinks below maxjobs, then it continues submitting new jobs. If you don't
> care about the number of submitted jobs (because your cluster does the
> scheduling anyway), you can just write
>
>
> "return" as the first line (before the "users = os." line).
>
>
> Still the submit block would have to be rewritten for slurm.
>
>
> Best, Martin
>
>
>
> Am 17.02.2018 um 12:13 schrieb Backhausen, Lea:
>
> Dear FS experts,
>
> I am trying to do a longitudinal analysis of around 250 adolescents with
> up to 4 data points each. Given the complexity I would like to use the
> long_submit_jobs script which is described here: https://surfer.nmr.mgh.
> harvard.edu/fswiki/FsTutorial/Scripts
>
> Unfourtunately it does only run on launchpad and I would do the analyses
> with SLURM using bash system.
> Has anybody adopted the script so i will run with SLURM or does anybody
> know where I should look to get information on this?
>
> I have little scripting experience so any help would be greatly
> appreciated!
>
> Best,
>
> Lea Backhausen, B.Sc.
>
> Research assistant
>
> Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie
> Tel. +49 (0)351 458-7166 <+49%20351%204587166>
> Fax +49 (0)351 458-5754 <+49%20351%204585754>
>
> Universitätsklinikum Carl Gustav Carus
> an der Technischen Universität Dresden
> Anstalt des öffentlichen Rechts des Freistaates Sachsen
> Fetscherstraße 74, 01307 Dresden
> *MailScanner has detected a possible fraud attempt from "deref-web-02.de"
> claiming to be* *http://www.uniklinikum-dresden.de*
> 
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
> Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image

[Satrajit Ghosh]

hey melanie,

awesome - if you've already done edits, it should be quite straightforward
to rerun with freesurfer 6. any chance you can run it through? otherwise i
can send you a filedrop link off the list.

cheers,

satra

On Thu, Oct 19, 2017 at 4:13 PM, Melanie Ganz  wrote:

> Hi Sean, Satra and Bruce,
>
> We just recently ran them all with v5.3 and did quite a few edits,
> especially to the subject ending in 10. Remember, we asked you for help,
> Bruce? 5
> I had asked before if someone was interested in us uploading the work
> since we took quite some care in doing it, but there was no answer. I can
> upload them to a Martinos file drop tomorrow morning if you want.
>
> Cheers,
> Mel
>
>
> On Oct 19, 2017 9:41 PM, Satrajit Ghosh  wrote:
>
> hi sean,
>
> i think i ran those in june 2013 at ohbm. however, my recollection of how
> it failed is encoded in that mail thread.
>
> it may be worthw hile to just run through those images with freesurfer 6.0.
>
> since it's only 6 brains, we can try running it through again.
>
> cheers,
>
> satra
>
> On Thu, Oct 19, 2017 at 3:29 PM, Bruce Fischl 
> wrote:
>
> Hi Seán
>
> I'm not sure. I think Satra posted the original issue, so maybe he knows.
> Satra?
>
>
> cheers
> Bruce
> On Thu, 19 Oct 2017, Seán Froudist Walsh wrote:
>
>
> Hi,
> Was the following issue ever solved? (sorry hit send too early!)
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html
> I tried and, like the previous two people it fails on mri_watershed.
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html
> Best wishes,
> Sean
>
> Hi Mike
>
> it's hard to say without looking at the data. if you upload the
> subject dir we will take a look
>
> Bruce
> On Thu, 24 Nov 2016, Michael Craig wrote:
>
> Hi All,
> I am trying to run recon-all on the Allen Brain Institute T1 images. It
> works
> without any issue on all but one subject (H0351.1009).
>
> I saw this post from a few years ago describing the exact problem I’m
> having,
> but don’t see a solution. Has anyone figured out how to get this subject
> to run
> in recon-all? Or is it simply a matter of there not being enough contrast
> between grey and white matter? Thanks for the help!
>
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-
> July/031482.html
>
> Best wishes,
> Mike
>
>
> On 19 October 2017 at 15:05, Seán Froudist Walsh  wrote:
>   Hi,
> Was the following issue ever solved?
>
>
>
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image

[Satrajit Ghosh]

hi sean,

i think i ran those in june 2013 at ohbm. however, my recollection of how
it failed is encoded in that mail thread.

it may be worthwhile to just run through those images with freesurfer 6.0.

since it's only 6 brains, we can try running it through again.

cheers,

satra

On Thu, Oct 19, 2017 at 3:29 PM, Bruce Fischl 
wrote:

> Hi Seán
>
> I'm not sure. I think Satra posted the original issue, so maybe he knows.
> Satra?
>
>
> cheers
> Bruce
> On Thu, 19 Oct 2017, Seán Froudist Walsh wrote:
>
>
>> Hi,
>> Was the following issue ever solved? (sorry hit send too early!)
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html
>> I tried and, like the previous two people it fails on mri_watershed.
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html
>> Best wishes,
>> Sean
>>
>> Hi Mike
>>
>> it's hard to say without looking at the data. if you upload the
>> subject dir we will take a look
>>
>> Bruce
>> On Thu, 24 Nov 2016, Michael Craig wrote:
>>
>> Hi All,
>> I am trying to run recon-all on the Allen Brain Institute T1 images. It
>> works
>> without any issue on all but one subject (H0351.1009).
>>
>> I saw this post from a few years ago describing the exact problem I’m
>> having,
>> but don’t see a solution. Has anyone figured out how to get this subject
>> to run
>> in recon-all? Or is it simply a matter of there not being enough contrast
>> between grey and white matter? Thanks for the help!
>>
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-J
>> uly/031482.html
>>
>> Best wishes,
>> Mike
>>
>>
>> On 19 October 2017 at 15:05, Seán Froudist Walsh  wrote:
>>   Hi,
>> Was the following issue ever solved?
>>
>>
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Repronim Training Workshop on Reproducible Research Nov 10-11 before SFN

[Satrajit Ghosh]

*ReproNim Training Workshop: Nov 10 full day - Nov 11 morning - George
Washington** University*

*Register and information at:* ​https://tinyurl.com/repronim-sfn17

*Purpose:*
The issue of lack of reproducibility has been described in several
scientific domains for several years, raising concerns specifically in the
life science community. ReproNim has developed a curriculum (
http://www.reproducibleimaging.org/#trai...
) that will give the students
the information, tools and practices to perform repeatable and efficient
research.

This training workshop will introduce material on the critical aspects of
reproducible brain imaging and will orient attendees using a hands on and
practical experience to conduct neuroimaging analyses with the next
generation of tools.

By the end of this course, the student will be aware of training materials
and concepts necessary to perform reproducible research in neuroimaging.
The student will be able to reuse these materials to conduct local
workshops and training and be able to customize the training for their
specific scenario.

*Prerequisites:*
If you are a student, postdoc or researcher in life science who directly
works with neuroimaging data - or wish to work with these data, and you
have some basic computational background, this training workshop is for
you. For instance, you should have already done either some R, or Python,
or Matlab or Shell scripting, or have used standard neuroimaging tools
(SPM, FSL, Afni, FreeSurfer, etc) and be engaged in neuroimaging research
projects. You should have already completed a neuroimaging analysis or know
how to do one.

*Logistics:*
*Location:* George Washington University, Marvin Center, Room 402-404
https://events-venues.gwu.edu/meeting-ro...

*Dates:* November 10-11, 2017.
*Costs:* Free - but space is limited - please apply for approval.
*Schedule:*
Friday November 10th:
8:30-9am: Introduction to the course and participants "setup"
9am-10:45: Reproducibility Basics (Module 0)
10:45-11am : Coffee break
11am-12:45 : FAIR data (Module 1)
12:45-2pm : Lunch+coffee
2pm-3:45: Data Processing (Module 2)
3:45-4pm: coffee break
4pm-5:45pm: Statistics for reproducible analyses (Module 3)
5:45-6:15: Questions and answers and feedback session
Saturday November 11th:
9am-12pm: The Re-executable Micro Publication Challenge
During this time, we will propose a small challenge around producing an
entirely re-executable neuroimaging analysis from fetching data to
producing statistical results. This will also be a time with close
interactions with neuroimaging experts in data handling and analysis.
12pm-12:30: Closing session: feedback and future: "become a trainer".

Weekly online office hours will be held prior to the workshop. Registered
attendees will receive information via email.

*Modules:*
*Module 0 - Reproducibility Basics:* Friday Nov. 10. 9am-10:45am.
This module guides through three somewhat independent topics, which are in
the heart of establishing and efficiently using common generic resources:
command line shell, version control systems (for code and data), and
distribution package managers. Gaining additional skills in any of those
topics could help you to not only become more efficient in your day-to-day
research activities, but also would lay foundation in establishing habits
to make your work actually more reproducible.

*Module 1 - FAIR Data:* Friday Nov. 10. 11am-12:45.
This module provides an overview of strategies for making research outputs
available through the web, with an emphasis on data. It introduces concepts
such persistent identifiers, linked data, the semantic web and the FAIR
principles. It is designed for those with little to no familiarity with
these concepts. More technical discussions can be found in the reference
materials.

*Module 2 - Data Processing:* Friday Nov. 10. 2pm-3:45pm.
This module teaches you to perform reproducible analysis, how to preserve
the information, and how to share data and code with others. We will show
an example framework for reproducible analysis, how to annotate, harmonize,
clean, and version brain imaging data, how to create and maintain
reproducible computational environments for analysis and use dataflow tools
to capture provenance and perform efficient analyses (docker) and other
tools.

*Module 3 - Statistics:* Friday 4am-5:45
The goal of this module is to teach brain imagers about the statistical
aspects of reproducibility. This module should give you a critical eye on
most of the current literature and the knowledge to do solid work,
understand exactly what is a p-value and its limitation to represent
evidence for results, practical notion of power and associated tools, etc.

*Instructors:* J. Bates, S. Ghosh, J. Grethe, Y. Halchenko, C. Haselgrove,
S. Hodge, D. Jarecka, D. Keator, D. Kennedy, M. Martone, N. Nichols, S.
Padhy, JB Poline, 

Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation

[Satrajit Ghosh]

hi ruchira,

while there is no freesurfer for windows, you can run freesurfer on windows
using docker or vagrant or the windows subsystem for unix (windows 10 pro
or better). i would recommend learning about these technologies first.
probably the most useful at this point would be to learn about docker (an
example tutorial here:
http://nipy.org/workshops/2017-03-boston/lectures/lesson-container/#1). if
you can install and run docker on your system, and become familiar with
docker, i would suggest using neurodocker (
https://github.com/kaczmarj/neurodocker) to create docker images for your
analysis needs. if there are general questions about neurodocker or docker
in neuroimaging, please post questions to neurostars.org.

cheers,

satra

On Sat, Aug 5, 2017 at 1:22 PM, Tabassum, Ruchira <
ruchira_tabas...@student.uml.edu> wrote:

> Hi,
>
>
>
> I need Freesurfer for my windows OS. Is there any windows version of
> FreeSurfer? Please let me know ASAP.
>
>
>
> Kind Regards
>
> Ruchira Tabassum
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing

[Satrajit Ghosh]

hi kirstie,

this makes python 2 a requirement for freesurfer as distributed. i've
started a PR that should at least help broaden the requirement to support
python 2 and 3.

https://github.com/freesurfer/freesurfer/pull/112

cheers,

satra

On Thu, Aug 3, 2017 at 3:41 AM, Kirstie Whitaker  wrote:

> Hi freesurfer team,
>
> I just ran into this error. I fixed it by switching from python 3.6 to
> python 2.7.
>
> Does this sound like the right fix? I wonder if it is documented somewhere
> on the wiki?
>
> Thank you for the great tool!
> Kx
>
> On 18 November 2016 at 21:14, Douglas N Greve 
> wrote:
>
>> what happens when you run  asegstats2table --help
>>
>> It does not fail for me. I wonder if it is a python version problem
>>
>>
>> On 11/18/2016 04:01 PM, Elijah Mak wrote:
>> > Hi ZK,
>> >
>> > Thanks. It is great news! I would like to report the following.
>> >
>> > asegstats2table seems to be acting strangely.
>> >
>> >  File "/Applications/freesurfer_b6/bin/asegstats2table", line 195
>> >
>> > print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
>> >
>> > Even typing asegstats2table --help leads to the same error message.
>> > It was not found in a prev dev built or in 5.3.
>> >
>> > Thanks.
>> >
>> > Also, not sure if it's placebo, but  freeview seems to be running
>> > quicker now.
>> >
>> > Best Wishes,
>> >
>> > Elijah
>> >
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
> Kirstie Whitaker, PhD
> Mozilla Fellow for Science
> 
>
> Postdoctoral researcher
> Department of Psychiatry
> University of Cambridge
>
> *Mailing Address*
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> *Phone: *+44 7583 535 307 <+44%207583%20535307>
> *Website:* www.kirstiewhitaker.com
> *Twitter:* @kirstie_j 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Nipype Workshop and Hackweek at MIT, March 27-31, 2017

[Satrajit Ghosh]

The Nipype development team will be holding a workshop and hackweek at MIT,
Cambridge, MA, USA, from March 27 - 31.

For details and registration see: http://nipy.org/workshops/
2017-03-boston/index.html

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Open Neuroimaging Laboratory

[Satrajit Ghosh]

Hi,

The Open Neuroimaging Laboratory (http://openneu.ro) was one of the six
finalists for the open science prize, and we presented our prototype
platform at the NIH BD2K open science symposium on Dec 1.

Check out our prototype for the #OpenSciencePrize and vote to help us
advance in the finals! www.OpenSciencePrize.org
 or https://goo.gl/o6dJRJ

The platform is also the first one in the brain imaging arena that allows
anyone to directly search for public data (some phenotypic and clinical
info and T1 images) and then curate (mostly T1/T2 images currently) using
an interactive, collaborative editor. We provide direct access to over 8k
MRIs. And we would encourage you to use it to curate public data together.
Every lab should not have to curate public data on their own, individually,
separately, and redundantly.

You can also upload your own images and freesurfer aseg or other
annotations and fix them online collaboratively. More importantly, as these
get fixed, we can use the cleaned data to start building better algorithms
as well.

To start, you can play with the thousands that are there (including an
excellent collection of brains from other species:
http://brainbox.pasteur.fr/project/braincatalogue/) and search for others
here (http://openneu.ro/metasearch).

any feedback is welcome. please post it here:
https://neurostars.org/t/open-neuroimaging-laboratory/17/1

cheers,

satra (on behalf of the Open Neuroimaging Laboratory)
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] avoiding FSL when using T2pial

[Satrajit Ghosh]

hi doug,

without hacking recon-all is there a way to avoid using FSL when using the
T2pial flag?

cheers,

satra

#@# Refine Pial Surfs w/ T2/FLAIR Sat Sep 24 08:42:34 UTC 2016

 bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta
/subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2

Log file is /subjects/sub-01/mri/transforms/T2raw.dat.log
Sat Sep 24 08:42:35 UTC 2016

setenv SUBJECTS_DIR /subjects
cd /subjects/sub-01/scripts
/opt2/freesurfer/bin/bbregister --s sub-01 --mov
/subjects/sub-01/mri/orig/T2raw.mgz --lta
/subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux b62492e050ac 4.4.20-moby #1 SMP Thu Sep 8 21:27:34 UTC 2016 x86_64
GNU/Linux
FREESURFER_HOME /opt2/freesurfer
mri_convert /subjects/sub-01/mri/orig/T2raw.mgz
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii
mri_convert /subjects/sub-01/mri/orig/T2raw.mgz
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /subjects/sub-01/mri/orig/T2raw.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.0675638, -0.9838, -0.166052)
j_ras = (0.119725, -0.173224, 0.977578)
k_ras = (0.990505, -0.0461684, -0.129489)
writing to
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii...
fslregister --s sub-01 --mov
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii --reg
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/reg.init.dat --niters 1
--maxangle 90 --nobetmov --tmp
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/fslregister --dof 6
--fsvol brainmask.mgz
ERROR: you must have the FSLDIR environment variable defined and pointing
to the FSL installation
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all with input T1s at different resolutions

[Satrajit Ghosh]

t voxel sizes.
  Currently not supported, maybe first make conform?
  Debug info: size(1) = 1, 1, 1.2   size(0) = 1, 1, 1
MultiRegistration::loadMovables: voxel size is different
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz.

Return code: 251
Interface RobustTemplate failed to run.

On Tue, May 31, 2016 at 2:38 PM, Bruce Fischl 
wrote:

> Hi Satra
>
> it will probably reject this by default, which you can get around be
> reslicing one of them to be like the other. Or "conforming" both of them.
>
> cheers
> Bruce
> On
> Tue, 31 May 2016, Satrajit Ghosh wrote:
>
> > hi folks,
> > does recon-all work if the input T1s for the same participant have
> different
> > resolutions? (i don't have a dataset to test, but trying to debug some
> > issues another group has been having).
> >
> > cheers,
> >
> > satra
> >
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] recon-all with input T1s at different resolutions

[Satrajit Ghosh]

hi folks,

does recon-all work if the input T1s for the same participant have
different resolutions? (i don't have a dataset to test, but trying to debug
some issues another group has been having).

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Seeking postdoctoral candidates for datascience positions

[Satrajit Ghosh]

We are seeking two postdoctoral computational/data scientists with a PhD in
computer science, electrical or biomedical engineering, neuroscience,
statistics, or related fields to apply for positions in the McGovern
Institute for Brain Research at Massachusetts Institute of Technology.

The projects cover a broad array of neuroinformatics.

- Datamining of gene-behavior-anatomy relationships
- Architecting next generation dataflow systems
- Reproducible research platforms and applications
- Nonlinear image and other high-dimensional registration
- Predictive analytics in mental health
- Linked data platforms

Working on these projects will involve collaboration partners within and
across regional and international institutions. Candidates are expected to
develop algorithms and prototype ideas, contribute to opensource tools, and
perform software engineering, testing, and validation. Candidates will have
the opportunity to mentor undergraduate and graduate students, and
contribute to datascience at MIT.

The ideal candidates will have strong computational skills, enjoy
collaborating, and be able to adapt to and adopt a diverse set of
technologies. A documented PhD in computer science, electrical or
biomedical engineering, neuroscience, statistics, or related field is
required before starting this position. Positions are available for one
year, with a possibility of yearly extension depending on performance and
funding.

For inquiries please contact Satrajit Ghosh (sa...@mit.edu).
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] reconstructing from T2 scan

[Satrajit Ghosh]

hi bruce,

we are missing a T1 scan from a participant. is there any pathway in
freesurfer to reconstruct from the T2-flair/flash scan?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch

[Satrajit Ghosh]

hi jens,

here is the post - the links were all broken, but i've updated them below.
note that this run was from nov 2013. i would recommend doing a run with
all the current patches installed.


an update on the files needed for a vanilla recon-all run (evaluation done
using cde:http://www.pgbovine.net/cde.html):

freesurfer files: https://www.dropbox.com/s/ei3m9dcvq8zemps/fslist.txt?dl=0
all files (fs + system+ output):
https://www.dropbox.com/s/1rjk7s0qyzn2hm5/allfiles.txt?dl=0
size of fs components (641M):
https://www.dropbox.com/s/mmcadnp63ao4dv8/size.txt?dl=0

one thing that surprised me a bit was that no component of fsaverage
appeared to be used (other than the directory being touched). this could be
something the program missed, or is actually true.


cheers,

satra

On Wed, Nov 19, 2014 at 5:03 PM, Jens Offenbach  wrote:

> Hi satra,
> I have tried to find some posts about the minimum files required to run
> recon-all, but I cannot find anything. Could you please try to find the
> post in the archives and provide me the link?
>
> Thank you very much!
>
>
>
> Gesendet: Mittwoch, 19. November 2014 um 15:23 Uhr
> Von: "Satrajit Ghosh" 
> An: "Freesurfer support list" 
> Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and
> 5.3.0-patch
>
> hi jens,
>
> if you search the archives, there is a post that lists the minimal set of
> files needed for running recon-all.
>
> i used a tool called cde to create it: http://www.pgbovine.net/cde.html
>
> this reduces the archive down to about 650MB comprising binaries and
> atlases.
>
> this wouldn't be for general purpose freesurfer processing, just for
> running recon-all.
>
>
> cheers,
>
> satra
>
> On Wed, Nov 19, 2014 at 8:40 AM, Jens Offenbach  wolle5...@gmx.de]> wrote:I have corresponding setup modules for
> auto-deployment and configuration in the cloud, but it still takes some
> time (even in the local cloud network) to transfer the archive from the
> fileserver to the virtual machine and especially to untar that archive. A
> manual untar took nearly 20 minutes, that's too slow for on-demand
> provisioning. I think the "subjects" folder can be removed. It seems to
> contain only example mri data, but I want to make sure not to remove
> anything that is actually required for analysis purposes. I need a minimum
> archive file which is able to perform the pipeline execution.
>
> Yes, we have a cloud portal, where different consumers can request the
> freesurfer service after uploading their mri raw files. The virtual
> machines are created and configured on the fly starting from a raw OS
> image. When the freesurfer run terminates the virtual machines are
> destroyed and the whole procedures starts again if someone requests a new
> freesurfer service (Create and start a virtual machine, transfer freesurfer
> archive, untar that archive, set environmement variables ...). We only want
> to parallelize different freesurfer jobs and not the freesurfer pipeline
> itself. We do not have a medical background.
>
> Regards,
> Jens
>
> Gesendet: Mittwoch, 19. November 2014 um 13:14 Uhr
> Von: "Krieger, Donald N." 
> An: "'Freesurfer support list'"  freesurfer@nmr.mgh.harvard.edu]>
> Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and
> 5.3.0-patch
>
> Dear Jens,
>
> I can offer just a bit of information and I also have a question.
> We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos
> 6 compiles work.
> The package appears to be self-contained as I have seen no faults on
> failures to find shared libraries.
> We simply untar freesurfer to a convenient location and set the PATH and
> FREESURFERHOME environment variables accordingly.
> I see no reason why that shouldn't work in a cloud solution except that I
> do not know what you have in mind as a use for your solution.
> Will there be a group of users who are provided access so that they can
> run freesurfer on an image data set through a portal to your cloud?
> Are you using the cloud to distribute the calculation to many machines?
> If so, what is the "granularity" of this, e.g. does one freesurfer run get
> one machine?
>
> Regards,
>
> Don
>
>
> Don Krieger, Ph.D.
> Department of Neurological Surgery
> University of Pittsburgh
> (412)648-9654 Office
> (412)521-4431 Cell/Text
>
>
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu[
> freesurfer-boun...@nmr.mgh.harvard.edu] [mailto:freesurfer-[freesurfer-]
> > boun...@nmr.mgh.harvard.edu[boun...@nmr.mgh.harvard.edu]] On Behalf Of
> Jens Offenbach
> > Sent: Wednesday, Nov

Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch

[Satrajit Ghosh]

hi jens,

if you search the archives, there is a post that lists the minimal set of
files needed for running recon-all.

i used a tool called cde to create it: http://www.pgbovine.net/cde.html

this reduces the archive down to about 650MB comprising binaries and
atlases.

this wouldn't be for general purpose freesurfer processing, just for
running recon-all.

cheers,

satra

On Wed, Nov 19, 2014 at 8:40 AM, Jens Offenbach  wrote:

> I have corresponding setup modules for auto-deployment and configuration
> in the cloud, but it still takes some time (even in the local cloud
> network) to transfer the archive from the fileserver to the virtual machine
> and especially to untar that archive. A manual untar took nearly 20
> minutes, that's too slow for on-demand provisioning. I think the "subjects"
> folder can be removed. It seems to contain only example mri data, but I
> want to make sure not to remove anything that is actually required for
> analysis purposes. I need a minimum archive file which is able to perform
> the pipeline execution.
>
> Yes, we have a cloud portal, where different consumers can request the
> freesurfer service after uploading their mri raw files. The virtual
> machines are created and configured on the fly starting from a raw OS
> image. When the freesurfer run terminates the virtual machines are
> destroyed and the whole procedures starts again if someone requests a new
> freesurfer service (Create and start a virtual machine, transfer freesurfer
> archive, untar that archive, set environmement variables ...). We only want
> to parallelize different freesurfer jobs and not the freesurfer pipeline
> itself. We do not have a medical background.
>
> Regards,
> Jens
>
> Gesendet: Mittwoch, 19. November 2014 um 13:14 Uhr
> Von: "Krieger, Donald N." 
> An: "'Freesurfer support list'" 
> Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and
> 5.3.0-patch
> Dear Jens,
>
> I can offer just a bit of information and I also have a question.
> We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos
> 6 compiles work.
> The package appears to be self-contained as I have seen no faults on
> failures to find shared libraries.
> We simply untar freesurfer to a convenient location and set the PATH and
> FREESURFERHOME environment variables accordingly.
> I see no reason why that shouldn't work in a cloud solution except that I
> do not know what you have in mind as a use for your solution.
> Will there be a group of users who are provided access so that they can
> run freesurfer on an image data set through a portal to your cloud?
> Are you using the cloud to distribute the calculation to many machines?
> If so, what is the "granularity" of this, e.g. does one freesurfer run get
> one machine?
>
> Regards,
>
> Don
>
>
> Don Krieger, Ph.D.
> Department of Neurological Surgery
> University of Pittsburgh
> (412)648-9654 Office
> (412)521-4431 Cell/Text
>
>
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> > boun...@nmr.mgh.harvard.edu] On Behalf Of Jens Offenbach
> > Sent: Wednesday, November 19, 2014 5:47 AM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and
> 5.3.0-
> > patch
> >
> > We are currently working on a solution that brings FreeSurfer in the
> cloud.
> > Unfortunately, we are facing a lot of problems. Hopefully, someone can
> help
> > me:
> >
> > I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is
> required to
> > download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu
> family?
> >
> > On the FTP server I have found a patch for 5.3.0, but I am not sure how
> to apply
> > it or if I must apply it? The Readme says to replace “mri_segstats”.
> What about
> > the other files “recon-all, fsfast, tksurferfv, …”?
> >
> > I want to reduce the archive to its bare minimum, otherwise the automated
> > deployment process takes too long. It should contain only those files
> which are
> > necessary to execute the pipeline without any viewer or examples. Which
> files
> > and folders can be deleted safely?
> >
> > The most important issue is to monitor the FreeSurfer pipeline
> execution. I know
> > that the scripts folder contains some status files which offer important
> data
> > helping me to monitor the pipeline execution progress of “recon-all”.
> > Unfortunately, that is not enough… If one step takes e.g. approximately
> 20
> > hours, I have to say something about the progress within this current
> step. Is
> > there any possibility to monitor the progress of a single step. We need
> > something that allows us to say e.g. that Step “CA Reg” has 34 % of its
> work
> > done so far which means that the overall pipeline progress is e.g. 63 %.
> Is it
> > possible to say that a specific step takes a specific portion of the
> overall
> > pipeline execution time. What influences this portion (format or quality
> of input,
> > 

Re: [Freesurfer] Open MP parallel processing scaling factor?

[Satrajit Ghosh]

hi andrew,

i haven't done many systematic comparisons but there are a few practical
considerations to take into account. in recon-all, i believe a few steps
are affected by the openmp option and that creates resource
underutilization. processors run idle when those steps are not being run.

in my ad hoc analysis i have found i can process a single subject in about
5 hours using openmp 8, but that holds up 8 processors for that subject.
the same subject can be processed in about 12 hours one 1 processor. say i
have 16 processors, i can process 16 subjects in say 12 hours using 1
processor per recon. however, using 8 per recon would take about 40 hours,
2 subjects every 5 hours.

so on our cluster, we tend to process with openmp 1 or 2 depending on the
average load on the cluster. this is also dependent on your hardware,
amount of memory, cluster scheduler, etc.,.

if i really need speed on an individual case i go with -openmp 8.

cheers,

satra

On Wed, Aug 20, 2014 at 11:04 AM, O'Shea,Andrew  wrote:

>  Hello all,
> Traditionally I have only processed FS data using a single core per
> person, but processing many people at once. Now we have caught up with the
> backlog of scans, we have a continuos trickle of scans coming in 1 by 1. I
> was wondering if anyone has tested how the speed-up of open-mp varies with
> number of cores used simultaneously. For example how much faster is using
> 100 cores versus 10? I am trying to find a sweet spot of resource usage and
> speed. Thanks!
> -Andrew
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] T2-space vs T2-space-FLAIR

[Satrajit Ghosh]

thanks bruce.

we aren't collecting the flair currently but some of our clinical
collaborators have asked for it. we are likely to collect both on our next
few participants, so happy to test out the alpha version.

cheers,

satra

On Wed, Jul 30, 2014 at 3:08 PM, Bruce Fischl 
wrote:

> please don't count on the T2 and FLAIR options doing the same thing as I
> suspect that they won't in the near future!
>
>
> Bruce
> On Wed, 30 Jul 2014, Satrajit Ghosh wrote:
>
>  thanks matt,
>> would like to be sure that your comments in relation to the T2-space-flair
>> sequence and not the typical clinical TSE-FLAIR. is that the case?
>>
>> cheers,
>>
>> satra
>>
>>
>> On Wed, Jul 30, 2014 at 2:23 PM, Matt Glasser  wrote:
>>   Bruce has said the FLAIR might be a little better for FreeSurfer
>>   but it’s worse for myelin maps (has less CNR for the myelin,
>>   though you can still see the major areas).  Currently, the T2
>>   and FLAIR flags do exactly the same thing, so it doesn’t even
>>   matter what flag you use.  I think it depends on what else you
>>   might want to do with the data (i.e. if myelin maps were
>>   important to your study you might go with T2w (like HCP), but if
>>   lesion detection were more important you might go with FLAIR
>>   (like biobank).
>>
>> Peace,
>>
>> Matt.
>>
>> From: Satrajit Ghosh 
>> Reply-To: Freesurfer support list 
>> Date: Wednesday, July 30, 2014 at 1:01 PM
>> To: Freesurfer Mailing List 
>> Subject: [Freesurfer] T2-space vs T2-space-FLAIR
>>
>> hi bruce,
>> is there any difference from freesurfer's perspective of using
>> T2-space or T2-space-flair?
>>
>> cheers,
>>
>> satra
>>
>> ___ Freesurfer mailing
>> list Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
>> information in this e-mail is intended only for the person to whom it
>> is addressed. If you believe this e-mail was sent to you in error and
>> the e-mail contains patient information, please contact the Partners
>> Compliance HelpLine at http://www.partners.org/complianceline . If the
>> e-mail was sent to you in error but does not contain patient
>> information, please contact the sender and properly dispose of the
>> e-mail.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] T2-space vs T2-space-FLAIR

[Satrajit Ghosh]

thanks matt.

cheers,

satra


On Wed, Jul 30, 2014 at 2:58 PM, Matt Glasser  wrote:

> Yes we performed both on the same subject in the same session and then
> compared the myelin map results.
>
> Peace,
>
> Matt.
>
> From: Satrajit Ghosh 
> Reply-To: Freesurfer support list 
> Date: Wednesday, July 30, 2014 at 1:53 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] T2-space vs T2-space-FLAIR
>
> thanks matt,
>
> would like to be sure that your comments in relation to the T2-space-flair
> sequence and not the typical clinical TSE-FLAIR. is that the case?
>
> cheers,
>
> satra
>
>
> On Wed, Jul 30, 2014 at 2:23 PM, Matt Glasser  wrote:
>
>> Bruce has said the FLAIR might be a little better for FreeSurfer but it’s
>> worse for myelin maps (has less CNR for the myelin, though you can still
>> see the major areas).  Currently, the T2 and FLAIR flags do exactly the
>> same thing, so it doesn’t even matter what flag you use.  I think it
>> depends on what else you might want to do with the data (i.e. if myelin
>> maps were important to your study you might go with T2w (like HCP), but if
>> lesion detection were more important you might go with FLAIR (like
>> biobank).
>>
>> Peace,
>>
>> Matt.
>>
>> From: Satrajit Ghosh 
>> Reply-To: Freesurfer support list 
>> Date: Wednesday, July 30, 2014 at 1:01 PM
>> To: Freesurfer Mailing List 
>> Subject: [Freesurfer] T2-space vs T2-space-FLAIR
>>
>> hi bruce,
>>
>> is there any difference from freesurfer's perspective of using T2-space
>> or T2-space-flair?
>>
>> cheers,
>>
>> satra
>>
>> ___ Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
>> information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Partners Compliance
>> HelpLine at http://www.partners.org/complianceline . If the e-mail was
>> sent to you in error but does not contain patient information, please
>> contact the sender and properly dispose of the e-mail.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
> ___ Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
> information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Partners Compliance
> HelpLine at http://www.partners.org/complianceline . If the e-mail was
> sent to you in error but does not contain patient information, please
> contact the sender and properly dispose of the e-mail.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] T2-space vs T2-space-FLAIR

[Satrajit Ghosh]

thanks matt,

would like to be sure that your comments in relation to the T2-space-flair
sequence and not the typical clinical TSE-FLAIR. is that the case?

cheers,

satra


On Wed, Jul 30, 2014 at 2:23 PM, Matt Glasser  wrote:

> Bruce has said the FLAIR might be a little better for FreeSurfer but it’s
> worse for myelin maps (has less CNR for the myelin, though you can still
> see the major areas).  Currently, the T2 and FLAIR flags do exactly the
> same thing, so it doesn’t even matter what flag you use.  I think it
> depends on what else you might want to do with the data (i.e. if myelin
> maps were important to your study you might go with T2w (like HCP), but if
> lesion detection were more important you might go with FLAIR (like
> biobank).
>
> Peace,
>
> Matt.
>
> From: Satrajit Ghosh 
> Reply-To: Freesurfer support list 
> Date: Wednesday, July 30, 2014 at 1:01 PM
> To: Freesurfer Mailing List 
> Subject: [Freesurfer] T2-space vs T2-space-FLAIR
>
> hi bruce,
>
> is there any difference from freesurfer's perspective of using T2-space or
> T2-space-flair?
>
> cheers,
>
> satra
>
> ___ Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
> information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Partners Compliance
> HelpLine at http://www.partners.org/complianceline . If the e-mail was
> sent to you in error but does not contain patient information, please
> contact the sender and properly dispose of the e-mail.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] T2-space vs T2-space-FLAIR

[Satrajit Ghosh]

hi bruce,

is there any difference from freesurfer's perspective of using T2-space or
T2-space-flair?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] HBM Hackathon - please distribute widely !

[Satrajit Ghosh]

The 2014 
Hackathon
registration
is 
open!
This unique 3-day event (June 5-7) will be held prior to annual meeting of
the Organization for Human Brain Mapping
(OHBM)at
the legendary
c-base , a decked-out collaborative art and technology
space at the heart of the Berlin hacker community. In keeping with the
spirit of prior neuroimaging hackathons such as OHBM
2013and
Brainhack  2012 and 2013,
participants will have the opportunity to propose collaborative projects
and engage in a number of open challenges.

For updated information on the developing Hackathon content, and to
contribute your own ideas, check out www.brainhack.org. Current projects
include the Sage Alzheimer’s Disease
Challenge,
cloud computing tutorials with
NITRC
- 
CEand
Amazon Web Services, workshops on data-sharing and meta-analysis, and
many others initiated by scientists from the brain imaging community (see
http:// 
brainhack.org
/categories/hackathon2014/ ).


Participants engaged in the Alzheimer’s Disease Challenge will have the
unique opportunity to set an initial benchmark for a multi-phase effort to
identify early accurate predictive biomarkers that can inform the
scientific, industrial and regulatory communities about the disease.

Join this vibrant community and help build open neuroscience initiatives in
one of the most unique tech venues in Berlin. To keep the collaborations
flowing, meals and refreshments are all included in the registration costs
and will be provided on-site, as well as $100+ in Amazon Web Service
credits for your computational needs. Participation is limited, so we
encourage you to register
now.


The spirit of the Hackathon will also be continuing into the OHBM meeting
in Hamburg from June 8-12, where a collaboration space will be available in
the conference venue. This space will be open to all OHBM attendees to
discuss, present, and continue working on hackathon projects.

OHBM Hackathon website: https://www.humanbrainmapping.org/hackathon

Registration:
https://www.humanbrainmapping.org/i4a/ams/conference/conference.cfm?conferenceID=98

Projects: http://www.brainhack.org/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] openmp/mkl support in tracula

[Satrajit Ghosh]

hi a.y.,

is there any part of tracula that currently benefits from openmp or mkl
availability?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] minimal data needed for maintaining edits

[Satrajit Ghosh]

to add a few more details:

i plan to run recon-all with a new version of freesurfer, but keep the
edits that were done and clean up the directory. would something like just
the following work for (recon-all -all -subjid subj):

subj/mri/orig.mgz
subj/mri/ctrl_pts.mgz
subj/mri/brainmask.mgz
subj/mri/wm.mgz

are there any other files i should keep to preserve edits? or are any of
the above not necessary?

two other ulterior motives:

1. create automated comparisons of freesurfer versions on this minimal data
2. share this minimal footprint when space is limited. (since edits take
time and are subjective, i'd like to provide those as part of data sharing).

cheers,

satra

On Wed, Apr 16, 2014 at 5:16 PM, Satrajit Ghosh  wrote:

> hi,
>
> some of our freesurfer directories have become bloated with all kinds of
> non-freesurfer data. if i want to rerun a subject in a new location while
> maintaining the edits, is there a minimal list of files i should copy over?
>
> cheers,
>
> satra
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] minimal data needed for maintaining edits

[Satrajit Ghosh]

hi,

some of our freesurfer directories have become bloated with all kinds of
non-freesurfer data. if i want to rerun a subject in a new location while
maintaining the edits, is there a minimal list of files i should copy over?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] tracula and libnetcdf

[Satrajit Ghosh]

hi folks,

we are setting up freesurfer on a new cluster and trying to be as modular
as possible in terms of dependencies. at present we are only installing
5.3.0 + tracula updates.

will libnetcdf (required by tracula) be included in freesurfer? or is it
considered a dependency?

and talking of which, is there a patch (a 5.3.1) in the horizon which will
include the tracula updates and perhaps netcdf in the freesurfer download.

cheers,

satra

On Wed, Feb 5, 2014 at 11:07 PM, Satrajit Ghosh  wrote:

> update: the lack of libnetcdf eventually makes it fail.
>
> i found a libnetcdf.so.7 on the cluster and soft linked it to
> libnetcdf.so.6 and added the path to LD_LIBRARY_PATH.
>
> that let trac-all -prep run to completion.
>
> cheers,
>
> satra
>
>
> On Wed, Feb 5, 2014 at 9:02 PM, Satrajit Ghosh  wrote:
>
>> hi a.y.,
>>
>> when running trac-preproc i'm getting this error (for dmri_motion and
>> dmri_group), but it continues running:
>>
>> /software/freesurfer/bin/dmri_motion: error while loading shared
>> libraries: libnetcdf.so.6: cannot open shared object file: No such file or
>> directory
>>
>> what will this fail to do?
>>
>> also is libnetcdf now a dependency for freesurfer? the reason i ask is
>> that i'm running this on a remote cluster for which i don't have admin
>> privileges.
>>
>> cheers,
>>
>> satra
>>
>>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Request for feedback on challenges/hurdles to using/learning Nipype

[Satrajit Ghosh]

hi all,

we are looking for feedback on learning/using/installing Nipype - any
challenge or hurdle that may have derailed you, wasted your time, left you
wanting a photon torpedo, etc.,.

we are in the process of re-architecting components of Nipype and feedback
would help a lot.

please post/discuss at:

http://neurostars.org/p/73/

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] tracula and libnetcdf

[Satrajit Ghosh]

update: the lack of libnetcdf eventually makes it fail.

i found a libnetcdf.so.7 on the cluster and soft linked it to
libnetcdf.so.6 and added the path to LD_LIBRARY_PATH.

that let trac-all -prep run to completion.

cheers,

satra


On Wed, Feb 5, 2014 at 9:02 PM, Satrajit Ghosh  wrote:

> hi a.y.,
>
> when running trac-preproc i'm getting this error (for dmri_motion and
> dmri_group), but it continues running:
>
> /software/freesurfer/bin/dmri_motion: error while loading shared
> libraries: libnetcdf.so.6: cannot open shared object file: No such file or
> directory
>
> what will this fail to do?
>
> also is libnetcdf now a dependency for freesurfer? the reason i ask is
> that i'm running this on a remote cluster for which i don't have admin
> privileges.
>
> cheers,
>
> satra
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] tracula and libnetcdf

[Satrajit Ghosh]

hi a.y.,

when running trac-preproc i'm getting this error (for dmri_motion and
dmri_group), but it continues running:

/software/freesurfer/bin/dmri_motion: error while loading shared libraries:
libnetcdf.so.6: cannot open shared object file: No such file or directory

what will this fail to do?

also is libnetcdf now a dependency for freesurfer? the reason i ask is that
i'm running this on a remote cluster for which i don't have admin
privileges.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] GPU considerations

[Satrajit Ghosh]

Does Freesurfer's GPU bits care about single or double precision?
Cheers, satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

[Satrajit Ghosh]

hi martin,

if you had one region you can use mri_segstats to extract for each voxel in
that roi, but not for multiple rois.

here is a snippet i use for timecourses in each roi.

https://github.com/nipy/nipype/blob/master/examples/rsfmri_preprocessing.py#L219

cheers,

satra


On Tue, Nov 5, 2013 at 5:30 PM, Martin Luessi
wrote:

> Hi,
>
> I have fMRI data which has been co-registered with the FS reconstruction
> using "bbregister". I would like to extract the voxel time series for
> the voxels in the subcortical labels from the "aseg" subcortical
> segmentation. I know that "mri_segstats" can be used with the "--avgwf"
> option to extract an average time series for each label, but is there a
> way to extract a time series for each voxel inside each label without
> averaging?
>
> Thanks,
>
> Martin
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] new version of mri_segstats

[Satrajit Ghosh]

thanks doug.

cheers,

satra

On Mon, Nov 4, 2013 at 5:33 PM, Douglas N Greve
wrote:

> It gives the same results as the 5.3 version. The difference is that it
> does not require the ribbon.mgz file to be there in order to run. If you
> run recon-all from start to finish, then there is not a problem. If you run
> recon-all partially, then it may fail because it runs mri_segstats before
> the ribbon.mgz is created.
> doug
>
>
>
>
> On 11/04/2013 09:30 AM, Satrajit Ghosh wrote:
>
>> hi doug,
>>
>> could you please highlight the changes - especially if there are any
>> critical bug fixes? and should we rerun the new mri_segstats on our current
>> 5.3 processed data?
>>
>> cheers,
>>
>> satra
>>
>> On Mon, Nov 4, 2013 at 9:26 AM, Douglas Greve 
>> > gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> I've put new versions here:
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
>> doug
>>
>>
>>
>> On 11/4/13 7:09 AM, Matura, Silke wrote:
>>
>>>
>>> Dear Freesurfer community,
>>>
>>> we are doing cortical thickness analyses with Freesurfer version
>>> 5.3.0 in a Linux environment.  In order to do the autorecon-1 and
>>> autorecon-2 steps, we need to download the new version of
>>> mri_segstats.
>>>
>>> Unfortunately, the link on the Freesurfer Release Notes Webpage
>>> does not work. Also, we could not find mri_segstats on the ftp
>>> server:
>>> /ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
>>> greve/mri_segstats.centos6/
>>>
>>> //
>>>
>>>
>>> Could you tell us, where we can download the new version of
>>> mri_segstats?
>>>
>>> Thank you,
>>>
>>> Silke
>>>
>>> Dr. Dipl.-Psych. Silke Matura
>>>
>>> Department of Psychiatry, Psychosomatic Medicine and Psychotherapy
>>>
>>> Laboratory of Neurophysiology and Neuroimaging
>>>
>>> Johann Wolfgang Goethe University of Frankfurt
>>>
>>> Heinrich-Hoffman-Str. 10
>>>
>>> 60528 Frankfurt Germany
>>>
>>> Tel: 069 6301 7655
>>>
>>> email: silke.mat...@kgu.de <mailto:silke.mat...@kgu.de>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu  <mailto:freesur...@nmr.mgh.
>>> harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu
>> >
>>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the
>> sender and properly
>> dispose of the e-mail.
>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] new version of mri_segstats

[Satrajit Ghosh]

hi doug,

could you please highlight the changes - especially if there are any
critical bug fixes? and should we rerun the new mri_segstats on our current
5.3 processed data?

cheers,

satra

On Mon, Nov 4, 2013 at 9:26 AM, Douglas Greve wrote:

>  I've put new versions here:
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
> doug
>
>
>
> On 11/4/13 7:09 AM, Matura, Silke wrote:
>
>  Dear Freesurfer community,
>
>
>
> we are doing cortical thickness analyses with Freesurfer version 5.3.0 in
> a Linux environment.  In order to do the autorecon-1 and autorecon-2 steps,
> we need to download the new version of mri_segstats.
>
> Unfortunately, the link on the Freesurfer Release Notes Webpage does not
> work. Also, we could not find mri_segstats on the ftp server: 
> *ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos6
> *
>
>
>
> Could you tell us, where we can download the new version of mri_segstats?
>
>
>
> Thank you,
>
> Silke
>
>
>
> Dr. Dipl.-Psych. Silke Matura
>
> Department of Psychiatry, Psychosomatic Medicine and Psychotherapy
>
> Laboratory of Neurophysiology and Neuroimaging
>
> Johann Wolfgang Goethe University of Frankfurt
>
> Heinrich-Hoffman-Str. 10
>
> 60528 Frankfurt Germany
>
> Tel: 069 6301 7655
>
> email: silke.mat...@kgu.de
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] minimal freesurfer pieces for recon-all

[Satrajit Ghosh]

hi,

an update on the files needed for a vanilla recon-all run (evaluation done
using cde: http://www.pgbovine.net/cde.html):

freesurfer files: https://www.dropbox.com/s/a56nzr3b7b8uqz6/fslist.txt
all files (fs + system+ output):
https://www.dropbox.com/s/1mhcuugb20cebod/allfiles.txt
size of fs components (641M):
https://www.dropbox.com/s/7yky56od4sf4bmi/size.txt

one thing that surprised me a bit was that no component of fsaverage
appeared to be used (other than the directory being touched). this could be
something the program missed, or is actually true.

cheers,

satra

On Sun, Nov 3, 2013 at 5:11 PM, Satrajit Ghosh  wrote:

> hi folks,
>
> has anybody on this list:
>
> a. built or extracted the necessary pieces (binaries, libraries, atlases)
> for running vanilla recon-all only?
>
> b. or better still, has a package file for any linux distro? i know the
> neurodebian folks are building one, but that's not fully ready yet.
>
> cheers,
>
> satra
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] difference in atlas size

[Satrajit Ghosh]

hi

i noticed a big discrepancy in size between these two, but not among other
lh and rh gcs files.

>  28769857 May 13 17:21 rh.DKTatlas100.gcs
>   6883965 May 13 17:21 lh.DKTatlas100.gcs

are these the intended sizes?

this is from the 5.3 centos6_x86_64 distro

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] minimal freesurfer pieces for recon-all

[Satrajit Ghosh]

hi folks,

has anybody on this list:

a. built or extracted the necessary pieces (binaries, libraries, atlases)
for running vanilla recon-all only?

b. or better still, has a package file for any linux distro? i know the
neurodebian folks are building one, but that's not fully ready yet.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_vol2surf clarification

[Satrajit Ghosh]

thanks very much doug.

cheers,

satra

On Tue, Oct 8, 2013 at 11:55 AM, Douglas N Greve
wrote:

>
> On 10/08/2013 09:17 AM, Satrajit Ghosh wrote:
> > hi folks,
> >
> > i'm using mri_vol2surf to map functional time series into
> > fsaverage3/4. my assumption is that each vertex time series will be
> > the mean over an icosahedral patch corresponding to the vertex on
> > fsaverage. is that how the resampling is done? also is the resampling
> > done with a single interpolation?
> If you spec fsaverageX as the target subject, then it first samples to
> the individual subject then runs surf2surf to map to fsaverageX. First,
> for each vertex on fsavergeX  it looks for the nearest neighbor in the
> individual. If fsaverageX is much sparser than the individual, then this
> will leave a bunch of vertices unused  in the individual. So it goes
> through a second step where it maps all the unused vertices in the
> individual to the closest vertex in fsaverageX. If a vertex in
> fsaverageX has multiple vertices from the individual, then the final
> value is the mean of the individual vertices (unless mapping volume or
> areal quantities in which case it gets the sum). You can control these
> options if you first map to the individual using  vol2surf then use
> surf2surf to map from individual to fsaverageX.
> doug
> >
> > if it's a single step, is there a way to project the interpolation
> > kernel corresponding to a vertex in fsaverage3 on the subject's own
> > surface?
> >
> > cheers,
> >
> > satra
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mri_vol2surf clarification

[Satrajit Ghosh]

hi folks,

i'm using mri_vol2surf to map functional time series into fsaverage3/4. my
assumption is that each vertex time series will be the mean over an
icosahedral patch corresponding to the vertex on fsaverage. is that how the
resampling is done? also is the resampling done with a single interpolation?

if it's a single step, is there a way to project the interpolation kernel
corresponding to a vertex in fsaverage3 on the subject's own surface?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Freesurfer surface circle of pre-defined size

[Satrajit Ghosh]

hi sarah,

you'll get a much quicker response posting PySurfer related questions to:

nipy-de...@neuroimaging.scipy.org

cheers,

satra

On Fri, Jul 26, 2013 at 12:57 PM,  wrote:

> Hello Freesurfer Experts,
>
> We would like to use PySurfer's function plot_label_foci.py to
> automatically create circular labels of a pre-defined radius (eg. 14mm) on
> the fsaverage surface of freesurfer.
>
> What are the specified units of "n_steps" in the command line argument
> "utils.coord_to_label(subject_id, coord, label='coord', hemi='lh',
> n_steps=50"?
>
> Thank you,
> Sarah
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Satrajit Ghosh]

thanks guys. any thoughts on when the ba*.stats files will use these? right
now i agree with bruce that they are biased by the predictability of the
region. less accurate prediction -> greater volume.

cheers,

satra


On Fri, Jul 26, 2013 at 10:28 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> There is a *.thresh.label version of all the BA labels in 5.3, but I don't
> think it's used by default. You can try using those labels instead.
>
>
> On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
>
>  hi bruce,
>> currently 5.3, but the data i was looking at was processed with 5.1 and in
>> that right ba44/45 was always larger.
>>
>> cheers,
>>
>> satra
>>
>>
>> On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl > >
>> wrote:
>>   Hi Satra,
>>
>>   what version are you using? I think Anastasia implemented a
>>   thresholded version in 5.3, but perhaps she can comment.
>>   Bruce
>>   On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
>>
>> hi bruce,
>> related to this question, how are the stats/volumes
>> of the BAs computed?
>>
>> cheers,
>>
>> satra
>>
>> On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Laouchedi
>>
>>   that is a big research question! The answer is
>> a qualified yes,
>>   but it depends strongly on what labels you
>> mean. In general we
>>   find that the closer you are to primary areas
>> like V1/M1, the
>>   stronger the correspondence is. We do supply
>> some explicit
>>   estimates of Brodmann areas, have you looked
>> at them?
>>
>>   Bruce
>>
>>
>>   On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
>>
>> Hi
>> i used freesurfer labels in a study
>> and i want
>> to identify the broadmann
>> areas corresponding to some labels, is
>> there any
>> correspondence between the
>> two ?
>>
>> Thanks
>>
>>
>>
>> __**_
>>   Freesurfer mailing list
>>   Freesurfer@nmr.mgh.harvard.edu
>>
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
>>   The information in this e-mail is intended
>> only for the person
>>   to whom it is
>>   addressed. If you believe this e-mail was sent
>> to you in error
>>   and the e-mail
>>   contains patient information, please contact
>> the Partners
>>   Compliance HelpLine at
>>   
>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>>  If
>> the e-mail was sent
>>   to you in error
>>   but does not contain patient information,
>> please contact the
>>   sender and properly
>>   dispose of the e-mail.
>>
>>
>>
>>
>>
>>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Satrajit Ghosh]

hi bruce,

currently 5.3, but the data i was looking at was processed with 5.1 and in
that right ba44/45 was always larger.

cheers,

satra


On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl wrote:

> Hi Satra,
>
> what version are you using? I think Anastasia implemented a thresholded
> version in 5.3, but perhaps she can comment.
> Bruce
>
> On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
>
>  hi bruce,
>> related to this question, how are the stats/volumes of the BAs computed?
>>
>> cheers,
>>
>> satra
>>
>> On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl > >
>> wrote:
>>   Hi Laouchedi
>>
>>   that is a big research question! The answer is a qualified yes,
>>   but it depends strongly on what labels you mean. In general we
>>   find that the closer you are to primary areas like V1/M1, the
>>   stronger the correspondence is. We do supply some explicit
>>   estimates of Brodmann areas, have you looked at them?
>>
>>   Bruce
>>
>>
>>   On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
>>
>> Hi
>> i used freesurfer labels in a study and i want
>> to identify the broadmann
>> areas corresponding to some labels, is there any
>> correspondence between the
>> two ?
>>
>> Thanks
>>
>>
>>   __**_
>>   Freesurfer mailing list
>>   Freesurfer@nmr.mgh.harvard.edu
>>   
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
>>   The information in this e-mail is intended only for the person
>>   to whom it is
>>   addressed. If you believe this e-mail was sent to you in error
>>   and the e-mail
>>   contains patient information, please contact the Partners
>>   Compliance HelpLine at
>>   
>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>>  If the e-mail was sent
>>   to you in error
>>   but does not contain patient information, please contact the
>>   sender and properly
>>   dispose of the e-mail.
>>
>>
>>
>>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Satrajit Ghosh]

hi bruce,

related to this question, how are the stats/volumes of the BAs computed?

cheers,

satra

On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl wrote:

> Hi Laouchedi
>
> that is a big research question! The answer is a qualified yes, but it
> depends strongly on what labels you mean. In general we find that the
> closer you are to primary areas like V1/M1, the stronger the correspondence
> is. We do supply some explicit estimates of Brodmann areas, have you looked
> at them?
>
> Bruce
>
>
> On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
>
>  Hi
>> i used freesurfer labels in a study and i want to identify the
>> broadmann
>> areas corresponding to some labels, is there any correspondence between
>> the
>> two ?
>>
>> Thanks
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Loading thickness data in python

[Satrajit Ghosh]

hi sebastian,

I would now like to create my own curvature overlay (similar to the
> thickness file) by assigning non-zero values to neighboring verteces to a
> selected vertex and zero to others. My question is: is there any way I can
> save a numpy array to a "morphometric" file using nibabel or a different
> package?
>

unfortunately write support is more sparse, but for something like this it
would not be difficult to add. a pull request on nibabel would be quite
welcome. you might even be able to peek at the matlab code to speed up the
translation to python.

cheers,

satra

On 15 July 2013 15:58, Satrajit Ghosh  wrote:
>
>> hi sebastian,
>>
>> you simply need to read the geometry file and the morphometry vector and
>> the two pieces will give you what you need.
>>
>> the geometry file gives you the relation between vertex indices via the
>> faces array.
>>
>> ```
>> def return_neighbors(faces, vertex_index):
>> faces_containing_vertex = np.nonzero((faces ==
>> vertex_index).sum(axis=1))[0]
>> neighbors = np.setdiff(faces[faces_containg_vertex, :].flatten(),
>> vertex_index)
>> return neighbors
>> ```
>>
>> cheers,
>>
>> satra
>>
>> On Mon, Jul 15, 2013 at 9:52 AM, Sebastian Urchs <
>> sebastian.ur...@gmail.com> wrote:
>>
>>> Hi Satra,
>>>
>>> thank you very much. I believe I have to rephrase my question as I
>>> didn't completely think it through. I need to find neighboring vertices to
>>> a specified vertex and then read out their thickness values. I don't think
>>> I can do this directly from the morphometry vector that pysurfer gives me.
>>>
>>> Thanks again, I'll send another mail to the mailinglist.
>>>
>>> Best,
>>> Sebastian
>>>
>>>
>>> On 15 July 2013 15:22, Satrajit Ghosh  wrote:
>>>
>>>> hi sebastian,
>>>>
>>>> please take a look at pysurfer (https://github.com/nipy/pysurfer) and
>>>> nibabel (https://github.com/nipy/nibabel).
>>>>
>>>> the relevant code is here:
>>>>
>>>> https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/io.py
>>>>
>>>> cheers,
>>>>
>>>> satra
>>>>
>>>> On Mon, Jul 15, 2013 at 9:11 AM, Sebastian Urchs <
>>>> sebastian.ur...@gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am trying to figure out how to load thickness data into python such
>>>>> that I would be able to identify the thickness at a given mesh node and
>>>>> also identify surrounding nodes. I searched the mailinglist and found this
>>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07307.html 
>>>>> but
>>>>> this unfortunately did not solve my question as I was unable to find a
>>>>> downloadable version of pymgh.
>>>>>
>>>>> Is there some python package that you could point me to and that
>>>>> allows me to load thickness data and do analysis in python?
>>>>>
>>>>> Thanks in advance!
>>>>> Sebastian
>>>>>
>>>>> ___
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>> The information in this e-mail is intended only for the person to whom
>>>>> it is
>>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>>> e-mail
>>>>> contains patient information, please contact the Partners Compliance
>>>>> HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>> you in error
>>>>> but does not contain patient information, please contact the sender
>>>>> and properly
>>>>> dispose of the e-mail.
>>>>>
>>>>>
>>>>
>>>
>>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Loading thickness data in python

[Satrajit Ghosh]

hi sebastian,

please take a look at pysurfer (https://github.com/nipy/pysurfer) and
nibabel (https://github.com/nipy/nibabel).

the relevant code is here:

https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/io.py

cheers,

satra

On Mon, Jul 15, 2013 at 9:11 AM, Sebastian Urchs
wrote:

> Hi,
>
> I am trying to figure out how to load thickness data into python such that
> I would be able to identify the thickness at a given mesh node and also
> identify surrounding nodes. I searched the mailinglist and found this
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07307.html but
> this unfortunately did not solve my question as I was unable to find a
> downloadable version of pymgh.
>
> Is there some python package that you could point me to and that allows me
> to load thickness data and do analysis in python?
>
> Thanks in advance!
> Sebastian
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] likelihood of identical subcortical volumes

[Satrajit Ghosh]

hi bruce,

i visualized these two subjects using freeview and nothing looked out of
the ordinary.

$ cat /mindhive/xnat/surfaces/adhd200/3684229/stats/aseg.stats | grep -i amy
 13  18  1764 1764.0  Left-Amygdala 64.7514
7.583136.90.54.
 28  54  1706 1706.0  Right-Amygdala64.3900
7.703611.89.78.
$ cat /mindhive/xnat/surfaces/adhd200/0010079/stats/aseg.stats | grep -i amy
 13  18  1543 1543.0  Left-Amygdala 58.6062
7.849731.90.59.
 28  54  1706 1706.0  Right-Amygdala60.1369
7.791431.84.53.

does this generation take partial volume into account? this is the default
output from running recon-all (from 5.1.0).

cheers,

satra


On Mon, Jul 8, 2013 at 5:14 PM, Bruce Fischl wrote:

> Hi Satra
>
> this seems vanishingly unlikely to me, particularly with partial volume
> correction. Have you visualize some of the subjects that have the same
> structure volume?
>
> Bruce
>
> On Mon, 8 Jul 2013, Satrajit Ghosh wrote:
>
>  a quick update. the following fiddle will show the number of subjects that
>> have an identical the same Right Amygdala volume. It simply plots a
>> histogram of the counts per volume (scroll to the bottom of the result
>> window).
>> http://fiddle.jshell.net/**satra/MXKY6/6/<http://fiddle.jshell.net/satra/MXKY6/6/>
>>
>> cheers,
>>
>> satra
>>
>>
>> On Mon, Jul 8, 2013 at 1:07 PM, Satrajit Ghosh  wrote:
>>   hi,
>>
>> trying to figure out the likelihood of identical subcortical volumes
>> across individuals. i'm noticing this in some data processed with
>> FreeSurfer 5.1.0.
>>
>> just to give some probabilities - these are out of about 963
>> participants.
>>
>> and there are several such small clusters of identical numbers - never
>> exceeding 6 participants i believe.
>>
>> cheers,
>>
>> satra
>> 0021003
>> aseg.stats
>> http://freesurfer.net/fswiki/**terms/Right-Hippocampus<http://freesurfer.net/fswiki/terms/Right-Hippocampus>
>> "4142.0"^^<http://www.w3.org/**2001/XMLSchema-datatypes#float<http://www.w3.org/2001/XMLSchema-datatypes#float>
>> **>
>> 0015035
>> aseg.stats
>> http://freesurfer.net/fswiki/**terms/Right-Hippocampus<http://freesurfer.net/fswiki/terms/Right-Hippocampus>
>> "4142.0"^^<http://www.w3.org/**2001/XMLSchema-datatypes#float<http://www.w3.org/2001/XMLSchema-datatypes#float>
>> **>
>> 3976121
>> aseg.stats
>> http://freesurfer.net/fswiki/**terms/Right-Hippocampus<http://freesurfer.net/fswiki/terms/Right-Hippocampus>
>> "4142.0"^^<http://www.w3.org/**2001/XMLSchema-datatypes#float<http://www.w3.org/2001/XMLSchema-datatypes#float>
>> **>
>> 1623716
>> aseg.stats
>> http://freesurfer.net/fswiki/**terms/Right-Amygdala<http://freesurfer.net/fswiki/terms/Right-Amygdala>
>> "1603.0"^^<http://www.w3.org/**2001/XMLSchema-datatypes#float<http://www.w3.org/2001/XMLSchema-datatypes#float>
>> **>
>> 0023005
>> aseg.stats
>> http://freesurfer.net/fswiki/**terms/Right-Amygdala<http://freesurfer.net/fswiki/terms/Right-Amygdala>
>> "1603.0"^^<http://www.w3.org/**2001/XMLSchema-datatypes#float<http://www.w3.org/2001/XMLSchema-datatypes#float>
>> **>
>> 0023008
>> aseg.stats
>> http://freesurfer.net/fswiki/**terms/Right-Amygdala<http://freesurfer.net/fswiki/terms/Right-Amygdala>
>> "1603.0"^^<http://www.w3.org/**2001/XMLSchema-datatypes#float<http://www.w3.org/2001/XMLSchema-datatypes#float>
>> **>
>> 0027025
>> aseg.stats
>> http://freesurfer.net/fswiki/**terms/Right-Amygdala<http://freesurfer.net/fswiki/terms/Right-Amygdala>
>> "1603.0"^^<http://www.w3.org/**2001/XMLSchema-datatypes#float<http://www.w3.org/2001/XMLSchema-datatypes#float>
>> **>
>> 1341865
>> aseg.stats
>> http://freesurfer.net/fswiki/**terms/Right-Amygdala<http://freesurfer.net/fswiki/terms/Right-Amygdala>
>> "1603.0"^^<http://www.w3.org/**2001/XMLSchema-datatypes#float<http://www.w3.org/2001/XMLSchema-datatypes#float>
>> **>
>> 2947936
>> aseg.stats
>> http://freesurfer.net/fswiki/**terms/Right-Amygdala<http://freesurfer.net/fswiki/terms/Right-Amygdala>
>> "1603.0"^^<http://www.w3.org/**2001/XMLSchema-datatypes#float<http://www.w3.org/2001/XMLSchema-datatypes#float>
>> **>
>>
>>
>>
>>

Re: [Freesurfer] likelihood of identical subcortical volumes

[Satrajit Ghosh]

a quick update. the following fiddle will show the number of subjects that
have an identical the same Right Amygdala volume. It simply plots a
histogram of the counts per volume (scroll to the bottom of the result
window).

http://fiddle.jshell.net/satra/MXKY6/6/

cheers,

satra


On Mon, Jul 8, 2013 at 1:07 PM, Satrajit Ghosh  wrote:

> hi,
>
> trying to figure out the likelihood of identical subcortical volumes
> across individuals. i'm noticing this in some data processed with
> FreeSurfer 5.1.0.
>
> just to give some probabilities - these are out of about 963 participants.
>
> and there are several such small clusters of identical numbers - never
> exceeding 6 participants i believe.
>
> cheers,
>
> satra
>
> 0021003aseg.statshttp://freesurfer.net/fswiki/terms/Right-Hippocampus
> "4142.0"^^<http://www.w3.org/2001/XMLSchema-datatypes#float>0015035
> aseg.statshttp://freesurfer.net/fswiki/terms/Right-Hippocampus "4142.0"^^<
> http://www.w3.org/2001/XMLSchema-datatypes#float>3976121aseg.stats
> http://freesurfer.net/fswiki/terms/Right-Hippocampus "4142.0"^^<
> http://www.w3.org/2001/XMLSchema-datatypes#float>
> 1623716aseg.statshttp://freesurfer.net/fswiki/terms/Right-Amygdala
> "1603.0"^^<http://www.w3.org/2001/XMLSchema-datatypes#float> 0023005
> aseg.statshttp://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
> http://www.w3.org/2001/XMLSchema-datatypes#float> 0023008aseg.stats
> http://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
> http://www.w3.org/2001/XMLSchema-datatypes#float> 0027025aseg.stats
> http://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
> http://www.w3.org/2001/XMLSchema-datatypes#float> 1341865aseg.stats
> http://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
> http://www.w3.org/2001/XMLSchema-datatypes#float> 2947936aseg.stats
> http://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
> http://www.w3.org/2001/XMLSchema-datatypes#float>
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] likelihood of identical subcortical volumes

[Satrajit Ghosh]

hi,

trying to figure out the likelihood of identical subcortical volumes across
individuals. i'm noticing this in some data processed with FreeSurfer 5.1.0.

just to give some probabilities - these are out of about 963 participants.

and there are several such small clusters of identical numbers - never
exceeding 6 participants i believe.

cheers,

satra

0021003aseg.statshttp://freesurfer.net/fswiki/terms/Right-Hippocampus
"4142.0"^^0015035
aseg.statshttp://freesurfer.net/fswiki/terms/Right-Hippocampus "4142.0"^^<
http://www.w3.org/2001/XMLSchema-datatypes#float>3976121aseg.stats
http://freesurfer.net/fswiki/terms/Right-Hippocampus "4142.0"^^<
http://www.w3.org/2001/XMLSchema-datatypes#float>
1623716aseg.statshttp://freesurfer.net/fswiki/terms/Right-Amygdala
"1603.0"^^ 0023005
aseg.statshttp://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
http://www.w3.org/2001/XMLSchema-datatypes#float> 0023008aseg.stats
http://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
http://www.w3.org/2001/XMLSchema-datatypes#float> 0027025aseg.stats
http://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
http://www.w3.org/2001/XMLSchema-datatypes#float> 1341865aseg.stats
http://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
http://www.w3.org/2001/XMLSchema-datatypes#float> 2947936aseg.stats
http://freesurfer.net/fswiki/terms/Right-Amygdala"1603.0"^^<
http://www.w3.org/2001/XMLSchema-datatypes#float>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] T2pial refinement bbregister error

[Satrajit Ghosh]

hey doug,

fslregister already uses flirt.fsl from freesurfer. you only need to
provide the schedule file and update the path. i just ran it copying the
schedule file over from fsl to a new location and setting the environment
variable FSLDIR, which i presume could be replaced with FREESURFER_HOME.
things ran fine to completion.

cheers,

satra

On Fri, Jul 5, 2013 at 2:14 PM, Douglas N Greve
wrote:

>
> I guess it is needed for fslregister. I suppose we could have it use the
> version of flirt that we distribute and also distribute the schedule files.
> doug
>
>
>
>
> On 07/05/2013 01:29 PM, Satrajit Ghosh wrote:
>
>> hi doug,
>>
>> same error with the updated one when i don't have FSL installed.
>>
>> writing to /data/subjects/H0351.2002/mri/**transforms/tmp.bbregister.**
>> 7856/template.nii...
>> fslregister --s H0351.2002 --mov /data/subjects/H0351.2002/mri/**
>> transforms/tmp.bbregister.**7856/template.nii --re
>> g 
>> /data/subjects/H0351.2002/mri/**transforms/tmp.bbregister.**7856/reg.init.dat
>> --niters 1 --maxangle 90 --tmp /dat
>> a/subjects/H0351.2002/mri/**transforms/tmp.bbregister.**7856/fslregister
>> --dof 6 --fsvol brainmask.mgz --nobetmov
>> ERROR: you must have the FSLDIR environment variable defined and pointing
>> to the FSL installation
>>
>> perhaps this is what's complaining in fslregister:
>>
>> ```
>>   if($DoTrans) then
>> if($?FSLDIR == 0) then
>>   echo "ERROR: you must have the FSLDIR environment variable defined
>> and pointing to the FSL installation"
>>   exit 1;
>> endif
>> if(! -e $FSLDIR/etc/flirtsch/xyztrans.**sch) then
>>   echo "ERROR: cannot find $FSLDIR/etc/flirtsch/xyztrans.**sch"
>>   exit 1;
>> endif
>>   endif
>> ```
>>
>> cheers,
>>
>> satra
>>
>>
>> On Fri, Jul 5, 2013 at 1:05 PM, Satrajit Ghosh > sa...@mit.edu>> wrote:
>>
>> thanks doug, i'll try that version right now.
>>
>> cheers,
>>
>> satra
>>
>> On Fri, Jul 5, 2013 at 11:37 AM, Douglas N Greve
>> > <mailto:gr...@nmr.mgh.harvard.**edu>>
>> wrote:
>>
>> I think the problem may be this:
>>
>> WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
>>
>> you can also update bbregister with the version here
>>
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>> greve/bbregister<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister>
>>
>>
>>
>> doug
>>
>>
>> On 07/05/2013 09:55 AM, Satrajit Ghosh wrote:
>> > hi doug,
>> >
>> > bbregister was running into an error trying to do T2pial
>> refinement
>> >
>> > sequence of commands and output here:
>> >
>> > 
>> https://gist.github.com/satra/**5934639<https://gist.github.com/satra/5934639>
>> >
>> > and it looks like the absence of FSLDIR
>> >
>> > i didn't have FSL installed on this machine - i thought that
>> > freesurfer had it's own version of flirt.
>> >
>> > is FSL necessary?
>> >
>> > cheers,
>> >
>> > satra
>> >
>> >
>> >
>> > __**_
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> 
>> <mailto:freesur...@nmr.mgh.**harvard.edu
>> >
>>
>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> <mailto:gr...@nmr.mgh.harvard.**edu
>> >
>>
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> 
>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> >
>> FileDrop: 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.ed

Re: [Freesurfer] T2pial refinement bbregister error

[Satrajit Ghosh]

hi doug,

same error with the updated one when i don't have FSL installed.

writing to
/data/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/template.nii...
fslregister --s H0351.2002 --mov
/data/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/template.nii
--re
g /data/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/reg.init.dat
--niters 1 --maxangle 90 --tmp /dat
a/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/fslregister --dof
6 --fsvol brainmask.mgz --nobetmov
ERROR: you must have the FSLDIR environment variable defined and pointing
to the FSL installation

perhaps this is what's complaining in fslregister:

```
  if($DoTrans) then
if($?FSLDIR == 0) then
  echo "ERROR: you must have the FSLDIR environment variable defined
and pointing to the FSL installation"
  exit 1;
endif
if(! -e $FSLDIR/etc/flirtsch/xyztrans.sch) then
  echo "ERROR: cannot find $FSLDIR/etc/flirtsch/xyztrans.sch"
  exit 1;
endif
  endif
```

cheers,

satra


On Fri, Jul 5, 2013 at 1:05 PM, Satrajit Ghosh  wrote:

> thanks doug, i'll try that version right now.
>
> cheers,
>
> satra
>
> On Fri, Jul 5, 2013 at 11:37 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> I think the problem may be this:
>>
>> WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
>>
>> you can also update bbregister with the version here
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
>>
>>
>>
>> doug
>>
>>
>> On 07/05/2013 09:55 AM, Satrajit Ghosh wrote:
>> > hi doug,
>> >
>> > bbregister was running into an error trying to do T2pial refinement
>> >
>> > sequence of commands and output here:
>> >
>> > https://gist.github.com/satra/5934639
>> >
>> > and it looks like the absence of FSLDIR
>> >
>> > i didn't have FSL installed on this machine - i thought that
>> > freesurfer had it's own version of flirt.
>> >
>> > is FSL necessary?
>> >
>> > cheers,
>> >
>> > satra
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] T2pial refinement bbregister error

[Satrajit Ghosh]

thanks doug, i'll try that version right now.

cheers,

satra

On Fri, Jul 5, 2013 at 11:37 AM, Douglas N Greve
wrote:

> I think the problem may be this:
>
> WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
>
> you can also update bbregister with the version here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
>
>
>
> doug
>
>
> On 07/05/2013 09:55 AM, Satrajit Ghosh wrote:
> > hi doug,
> >
> > bbregister was running into an error trying to do T2pial refinement
> >
> > sequence of commands and output here:
> >
> > https://gist.github.com/satra/5934639
> >
> > and it looks like the absence of FSLDIR
> >
> > i didn't have FSL installed on this machine - i thought that
> > freesurfer had it's own version of flirt.
> >
> > is FSL necessary?
> >
> > cheers,
> >
> > satra
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] failure on 1 of the allen institute brains

[Satrajit Ghosh]

hi bruce,

mri_watershed failed.

cheers,

satra


 mri_watershed -T1 -brain_atlas
/nitrc/usr/local/freesurfer//average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz


Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for
details)

*
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed

*WATERSHED**
Sorting...
  first estimation of the COG coord: x=127 y=129 z=144 r=65
  first estimation of the main basin volume: 1176865 voxels
  Looking for seedpoints
2 found in the cerebellum
15 found in the rest of the brain
  global maximum in x=102, y=106, z=114, Imax=255
  CSF=12, WM_intensity=110, WM_VARIANCE=5
  WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
  preflooding height equal to 10 percent
done.
Analyze...

  main basin size=19240706014 voxels, voxel volume =1.000
 = 19240706014 mmm3 = 19240706.048 cm3
done.
PostAnalyze...Basin Prior
 0 basins merged thanks to atlas
  * 0 basin(s) merged in 1 iteration(s)
  * 0 voxel(s) added to the main basin
done.
Weighting the input with prior template

TEMPLATE DEFORMATION

  second estimation of the COG coord: x=128,y=136, z=125, r=9654
iterations
 couldn't find WM with original limits - expanding ^^

mri_watershed Error:
 GLOBAL region of the brain empty !


On Fri, Jul 5, 2013 at 10:03 AM, Bruce Fischl wrote:

> Hi Satra
>
> what was the error? Pretty poor gray/white contrast in the data.
>
> cheers
> Bruce
>
>
> On Fri, 5 Jul 2013, Satrajit Ghosh wrote:
>
>  hi bruce and others:
>>
>> i'm getting a recon failure on this particular brain: H0351.1009
>>
>> the quality isn't great, but if you can take a quick look at the brain to
>> see if you can spot any particular issues, that would be great.
>>
>> 4 of the others finished recon and 3 are almost there.
>>
>> cheers,
>>
>> satra
>>
>> data location: 
>> http://human.brain-map.org/**mri_viewers/data<http://human.brain-map.org/mri_viewers/data>
>>
>> command:  recon-all -subjid H0351.1009 -all -i
>> /data/allen/H0351.1009/T1.nii.**gz -openmp 8 -notalairach
>>
>> ==> /data/subjects/H0351.1009/**scripts/recon-all-status.log <==
>> status file for recon-all
>> Fri Jul  5 00:02:39 UTC 2013
>> #@# MotionCor Fri Jul  5 00:02:43 UTC 2013
>> #@# Nu Intensity Correction Fri Jul  5 00:02:57 UTC 2013
>> #@# Intensity Normalization Fri Jul  5 00:04:45 UTC 2013
>> #@# Skull Stripping Fri Jul  5 00:07:53 UTC 2013
>> Linux node007 3.2.0-39-virtual #62-Ubuntu SMP Thu Feb 28 00:48:27 UTC 2013
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s H0351.1009 exited with ERRORS at Fri Jul  5 00:16:26 UTC 2013
>>
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>  If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] T2pial refinement bbregister error

[Satrajit Ghosh]

hi doug,

bbregister was running into an error trying to do T2pial refinement

sequence of commands and output here:

https://gist.github.com/satra/5934639

and it looks like the absence of FSLDIR

i didn't have FSL installed on this machine - i thought that freesurfer had
it's own version of flirt.

is FSL necessary?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] failure on 1 of the allen institute brains

[Satrajit Ghosh]

hi bruce and others:

i'm getting a recon failure on this particular brain: H0351.1009

the quality isn't great, but if you can take a quick look at the brain to
see if you can spot any particular issues, that would be great.

4 of the others finished recon and 3 are almost there.

cheers,

satra

data location: http://human.brain-map.org/mri_viewers/data

command:  recon-all -subjid H0351.1009 -all -i
/data/allen/H0351.1009/T1.nii.gz -openmp 8 -notalairach

==> /data/subjects/H0351.1009/scripts/recon-all-status.log <==
status file for recon-all
Fri Jul  5 00:02:39 UTC 2013
#@# MotionCor Fri Jul  5 00:02:43 UTC 2013
#@# Nu Intensity Correction Fri Jul  5 00:02:57 UTC 2013
#@# Intensity Normalization Fri Jul  5 00:04:45 UTC 2013
#@# Skull Stripping Fri Jul  5 00:07:53 UTC 2013
Linux node007 3.2.0-39-virtual #62-Ubuntu SMP Thu Feb 28 00:48:27 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s H0351.1009 exited with ERRORS at Fri Jul  5 00:16:26 UTC 2013
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [tracula] running into trouble with nifti data

[Satrajit Ghosh]

hi ay,

so this is what i did. i flipped the gradient LR intentionally, ran
flip4fsl and then dtifit and now the eigenvec 1 looks good, but not if i
run dtifit prior to flip4fsl.

but this brings me back to my original point which is that my image and the
gradients are (i think) already in proper orientation for fsl tools (since
the preflip output in the previous email looks correct) and flip4fsl is
making it inappropriate for fsl.

also as some additional info:
- yes this is the siemens 60 dir scan but that predefined gradient table
doesn't take into account the slice orientation
- if you use dcm2nii to extract these dicoms, the first two gradients are:

0.996362388134 0.0389195755124 -0.07581084221601
-0.65292024612426  0.00993375014513 -0.75736147165298

this is because dcm2nii, much like DTIPrep takes the image orientation
matrix into account when doing the conversion, which mri_convert doesn't.

so i think tracula should have an option of not flipping 4 fsl in the
scenario where other processes (e.g., my script, dcm2nii) automatically
take care of generating an fsl compatible file + gradient info.

please let me know if i'm misinterpreting something here.

cheers,

satra

On Tue, Jul 2, 2013 at 8:21 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Satra - What you're showing in the screenshots would be consistent with
> a L-R flip of the gradient directions, which is what my comparison of your
> gradients to the original Siemens gradients indicated. (Assuming the data
> was acquired with the standard Siemens 60 gradient directions.)
>
>
> a.y
>
> On Tue, 2 Jul 2013, Satrajit Ghosh wrote:
>
>  hi ay,
>> i'll look into the orientations a little later tonight, but here is V1
>> overlaid on FA for preflip and postflip execution of dtifit.
>>
>> cheers,
>>
>> satra
>>
>>
>> On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What
>>   flip4fsl will do is convert it to LAS, and perform the same
>>   conversion on the gradient table that you provide. This of
>>   course assumes that dwi_orig.nii.gz and your gradient table are
>>   consistent as they come out of your custom preprocessing. Is
>>   there any chance that they're not?
>>
>>   Looking at the sample data set that you sent me, I can only see
>>   what came out of your preprocessing and not what went in. I'm
>>   assuming that this is from the standard Siemens 60 direction
>>   sequence, and it has 57 directions b/c 3 of them were thrown out
>>   by your preprocessing. I don't know which directions were thrown
>>   out obviously, but the first 2 directions in your gradient table
>>   are:
>>   -0.99699027939850948 -0.057720153020443053 0.051758263409041924
>>   0.63287878858184599 0.066164234845749903 0.77141869630019422
>>
>>   The first two directions in the Siemens 60 direction gradient
>>   table are:
>>   1.00  0.00  0.00
>>   0.5867917880 -0.3765825401 -0.7168409782
>>
>>   There's not only a small adjustment of the direction but also a
>>   sign change there. So I'd look into that.
>>
>>   Let me know if any of my assumptions about your original data is
>>   wrong.
>>
>>   a.y
>>
>>   On Tue, 2 Jul 2013, Satrajit Ghosh wrote:
>>
>> hi anastasia,
>> i'm trying to debug a seg fault that some folks are
>> seeing deep into a
>> tracula run.
>>
>> process:
>>
>> 1. feed dicoms to a script that runs DTIPrep and
>> outputs a nifti file, bvec,
>> bval
>>
>> (among checking for many artifacts, this reduces the
>> b=0 volumes to a single
>> registered mean volume, runs eddy correction,
>> discards bad directions,
>> reorients the gradients appropriately and generates
>> a report of the quality)
>>
>> 2. run tracula on this nifti file
>>
>> observation:
>>
>> when i run fsl/dtifit on the same nifti file + bvec
>> + bval, i get the proper
>> orientation for eigvec1 lines. however, when i feed
>> this into tracula, the
>> output of the dtifit step looks terrible - i.e. the
>> lines are not oriented
>> as how one might expect water to diffuse.
>>

[Freesurfer] [tracula] running into trouble with nifti data

[Satrajit Ghosh]

hi anastasia,

i'm trying to debug a seg fault that some folks are seeing deep into a
tracula run.

process:

1. feed dicoms to a script that runs DTIPrep and outputs a nifti file,
bvec, bval

(among checking for many artifacts, this reduces the b=0 volumes to a
single registered mean volume, runs eddy correction, discards bad
directions, reorients the gradients appropriately and generates a report of
the quality)

2. run tracula on this nifti file

observation:

when i run fsl/dtifit on the same nifti file + bvec + bval, i get the
proper orientation for eigvec1 lines. however, when i feed this into
tracula, the output of the dtifit step looks terrible - i.e. the lines are
not oriented as how one might expect water to diffuse.

suspicion:

although i have not reached the crash yet, i believe it might be related to
this fact that the gradients are not oriented properly relative to the
volume.

i also suspect that this has something to do with the flip4fsl step inside
tracula, which is possibly unnecessary because fsl already likes the input
files. but it seems this step is encoded quite heavily within the trac-all
scripts.

questions:

a. is there a quick way to turn the flip4fsl step off?
b. alternatively do you have any suggestions for what to do here?

the whole point of running through DTIPrep is to clean up the data before
giving it to tracula or other programs, so i would really like to keep that
step.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Technical Assistant Position Available at MIT

[Satrajit Ghosh]

For details of the position and for applying see:

http://sh.webhire.com/servlet/av/jd?ai=631&ji=2681168&sn=I
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Transform SMOOTHWM to DTI B0

[Satrajit Ghosh]

hi dan,

if you use bbregister to match the DTI b0 to freesurfer space, then you can
transform the surface back (no guarantees on the tesselations though i
think). the only additional component here would be a tkr transform that's
based on the conformed space. i might even have some python code lying
around to do this. i'll take a look.

cheers,

satra

On Thu, Apr 11, 2013 at 10:40 AM, Daniel Haehn <
daniel.ha...@childrens.harvard.edu> wrote:

> Hi all,
>
> I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space.
>
> I found
> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms but
> this describes transforming the B0 to T1 space and then match the surfaces.
> I don't want to change the DTI B0 image.
>
>  What is the best way to do that?
>
> Thank you very much!
> Daniel
>
> --
> Daniel Haehn
> FNNDSC / BCH
> +1.857.218.5140
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] fsaverage mappings

[Satrajit Ghosh]

hi folks,

are there predefined mappings between the fsaverage surfaces? for example,
i have an array of numbers for all the vertices in fsaverage4. is there an
easy way to map those to vertices on to fsaverage/fsaverage5/... without
going through surf2surf? something perhaps implemented in matlab or python.

e.g., 1->1, 2->1, 3->1, ... 10->2, 11->2, ...

i believe fsaverage 6/5/4/3 are icosahedral subsampling of fsaverage -- can
i find this mapping somewhere or create it somehow?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] 5.2 ami

[Satrajit Ghosh]

hi all,

is there a public ami with freesurfer 5.2 available?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] fsaverage across versions

[Satrajit Ghosh]

thanks bruce. indeed, we are not expecting identical output and in these
cases that we are looking at it's all 5.x for most part.

cheers,

satra

On Mon, Feb 4, 2013 at 9:34 AM, Bruce Fischl wrote:

> Hi Satra,
>
> certainly fsaverage will change if we change things in spherical
> registration, or potentially elsewhere. I don't anticipate any large
> changes, but I wouldn't count on them being identical
> Bruce
>
> On Mon, 4 Feb 2013, Satrajit Ghosh wrote:
>
>  hi bruce and others,
>> are there any specific implications we should be worried about (e.g.,
>> with qdec or surf2surf) when using an fsaverage
>> that's from a different version that ran the recon.
>>
>> cheers,
>>
>> satra
>>
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>  If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] fsaverage across versions

[Satrajit Ghosh]

hi bruce and others,

are there any specific implications we should be worried about (e.g., with
qdec or surf2surf) when using an fsaverage that's from a different version
that ran the recon.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] expected directory structure

[Satrajit Ghosh]

thanks doug,

that's what i ended up doing. once i'm done, i might run it by you'll to
make sure i'm not misinterpreting any of the files.

cheers,

satra

On Mon, Jan 7, 2013 at 12:51 PM, Douglas N Greve
wrote:

> Hi Satra, I don't think we've ever compiled such a thing. Maybe just run
> recon-all and then ls -lR :)
> doug
>
>
> On 01/05/2013 02:48 PM, Satrajit Ghosh wrote:
> > hi folks,
> >
> > happy new year.
> >
> > we are trying to create an object model for the freesurfer directory.
> >
> > is there a function/script in freesurfer that would return me
> > effectively something `ls -lR` but only the items that are mandatory
> > for a subjects' directory?
> >
> > if not, is there a document that lists the relevant outputs along the
> > lines of something like this:
> >
> > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#FEAT_Output
> >
> > and if anybody is interested, here is our work in progress in
> > cataloging freesurfer directory structure and stats (coming soon) in
> > the w3c-prov model format.
> >
> >
> http://nbviewer.ipython.org/urls/dl.dropbox.com/s/1ssv4i1dyraa46h/freesurfer_catalog.ipynb
> >
> > (the link doesn't have versioning yet - but will keep changing as we
> > work on it)
> >
> > cheers,
> >
> > satra
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] expected directory structure

[Satrajit Ghosh]

hi folks,

happy new year.

we are trying to create an object model for the freesurfer directory.

is there a function/script in freesurfer that would return me effectively
something `ls -lR` but only the items that are mandatory for a subjects'
directory?

if not, is there a document that lists the relevant outputs along the lines
of something like this:

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#FEAT_Output

and if anybody is interested, here is our work in progress in cataloging
freesurfer directory structure and stats (coming soon) in the w3c-prov
model format.

http://nbviewer.ipython.org/urls/dl.dropbox.com/s/1ssv4i1dyraa46h/freesurfer_catalog.ipynb

(the link doesn't have versioning yet - but will keep changing as we work
on it)

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Satrajit Ghosh]

thanks matt and bruce. this is very helpful.

cheers,

satra

On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl wrote:

> yes, that's probably true. The FLAIR we use is just a T2-SPACE scan with
> an inversion pulse to put CSF at the null point, so if you can get T2-space
> at .7 you should be able to get FLAIR (although you do burn some SNR with
> the inversion)
>
>
> On Tue, 20 Nov 2012, Matt Glasser wrote:
>
>  Hi Bruce,
>>
>> Can you get good FLAIRs at 0.7mm isotropic?
>>
>> The fluid thing makes sense for surface reconstruction, but I think it
>> would mess up myelin maps if someone also wanted to do that using the
>> ratio method.  If the CSF is now dark and you divide the dark CSF in the
>> T1w with dark CSF in the T2w, you would get unpredictable results in the
>> partial volume region along the edge.
>>
>> Thanks,
>>
>> Matt.
>>
>> On 11/20/12 6:27 PM, "Bruce Fischl"  wrote:
>>
>>  Hi Satra
>>>
>>> the T1 maps accomplish much of what the ratio does - it gets rid of
>>> receive bias effects. I'm not really sure which is better. They are about
>>> the same amount of scan time.
>>>
>>> The advantage of including the flair inversion pulse in the T2 space is
>>> that it nulls fluid and lets intensities by monotonically decreasing
>>> moving
>>> outwards from the gray/white boundary. This makes partial volume effects
>>> less of a problem. Dura is also pretty much totally absent from the FLAIR
>>> and in the prelim data that we've processed having the FLAIR images lets
>>> the surface recover from pretty much all mistakes in which dura is
>>> included
>>> in the pial surface.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>>
>>> On Tue, 20 Nov 2012, Matt Glasser wrote:
>>>
>>>  If you make a T1 map you can use that to look at differences in myelin
>>>> content, but I don't know all of the ways to calculate T1 or if you
>>>> could
>>>> get that from only two flip angles.  Two images with roughly the same
>>>> contrast won't work for the ratio method.  You need to have opposite
>>>> contrast.
>>>>
>>>> Also I'm not sure how a FLAIR would be better than a T2-SPACE.
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: Satrajit Ghosh 
>>>> Date: Tuesday, November 20, 2012 5:51 PM
>>>> To: Matt Glasser 
>>>> Cc: "Watson, Christopher" 
>>>> 
>>>> >,
>>>> "Winter, Warren" 
>>>> 
>>>> >,
>>>> "freesur...@nmr.mgh.harvard.**edu " <
>>>> freesur...@nmr.mgh.harvard.**edu >
>>>> Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
>>>> surface recons?
>>>>
>>>> hi
>>>> matt: could you generate the myelin maps say from two flash scans at
>>>> different flip angles?
>>>> bruce: if one had a choice between an mprage + t2 flair and 2 flash
>>>> scans at
>>>> 5/20 flip angles, what would be your recommendation?
>>>>
>>>> cheers,
>>>>
>>>> satra
>>>>
>>>> On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser  wrote:
>>>>   If you get an MPRAGE and T2-SPACE you can make myelin maps too.
>>>>   FreeSurfer's final surface placement benefits a lot from high
>>>>   resolution
>>>>   images (less than 1mm) and you can still get good SNR with when
>>>>   you use
>>>>   32-channel coils.
>>>>
>>>>   Peace,
>>>>
>>>>   Matt.
>>>>
>>>>   On 11/20/12 4:41 PM, "Bruce Fischl" 
>>>>   wrote:
>>>>
>>>>  >Yes, definitely. The t2-space flair is a big help
>>>>  >
>>>>  >
>>>>  >
>>>>  >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher"
>>>>  
>>>> >>
>>>> wrote:
>>>>  >
>>>>  >> Hi Bruce,
>>>>  >> So would you recommend acquiring a T2 in addition to an
>>>>  >>(ME)MPRAGE/SPGR? i.e. is it worth squeezing another
>>>>   acquisition into a
>>>>  >>protocol?
>>>>  >>
>>>&g

Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Satrajit Ghosh]

hi

matt: could you generate the myelin maps say from two flash scans at
different flip angles?

bruce: if one had a choice between an mprage + t2 flair and 2 flash scans
at 5/20 flip angles, what would be your recommendation?

cheers,

satra

On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser  wrote:

> If you get an MPRAGE and T2-SPACE you can make myelin maps too.
> FreeSurfer's final surface placement benefits a lot from high resolution
> images (less than 1mm) and you can still get good SNR with when you use
> 32-channel coils.
>
> Peace,
>
> Matt.
>
> On 11/20/12 4:41 PM, "Bruce Fischl"  wrote:
>
> >Yes, definitely. The t2-space flair is a big help
> >
> >
> >
> >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher"
> > wrote:
> >
> >> Hi Bruce,
> >> So would you recommend acquiring a T2 in addition to an
> >>(ME)MPRAGE/SPGR? i.e. is it worth squeezing another acquisition into a
> >>protocol?
> >>
> >> Chris
> >> 
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu
> >>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> >>[fis...@nmr.mgh.harvard.edu]
> >> Sent: Tuesday, November 20, 2012 3:01 PM
> >> To: Winter, Warren
> >> Cc: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
> >>surface recons?
> >>
> >> Hi Warren
> >>
> >> yes, it will be part of the upcoming 5.2 release, hopefully in Dec. It
> >> will use either a FLAIR or T2 (ideally T2-SPACE for either one)
> >>
> >> cheers
> >> Bruce
> >> On Tue, 20
> >> Nov 2012, Winter, Warren wrote:
> >>
> >>> Hi all,
> >>>
> >>> Back in January and October Bruce mentioned that he had under
> >>>development some scripts designed to utilize T2-SPACE images for better
> >>>pial surface reconstruction in the presence of dura -- I was just
> >>>wondering if any of that is ready for trial?
> >>>
> >>> Thanks!
> >>>
> >>> Warren
> >>>
> >>> --
> >>> Warren Winter
> >>> Research Coordinator
> >>> Boston Children's Hospital
> >>> Sheridan Laboratory of Cognitive Neuroscience
> >>> Division of Developmental Medicine
> >>> 1 Autumn Street, AU 650
> >>> Boston, MA 02215
> >>> 857-218-5224
> >>>
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> The information in this e-mail is intended only for the person to whom
> >>it is
> >> addressed. If you believe this e-mail was sent to you in error and the
> >>e-mail
> >> contains patient information, please contact the Partners Compliance
> >>HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to you
> >>in error
> >> but does not contain patient information, please contact the sender and
> >>properly
> >> dispose of the e-mail.
> >>
> >>
> >>
> >
> >___
> >Freesurfer mailing list
> >Freesurfer@nmr.mgh.harvard.edu
> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

[Satrajit Ghosh]

hi doug,

just to follow up on this. if i had the phase encode direction (we
currently store various dicom attributes in a nifti header extension),
where would i provide it?

cheers,

satra

On Tue, Nov 13, 2012 at 11:27 AM, Douglas N Greve  wrote:

> Hi Clark, the phase encode direction is always lost since that
> information is not represented in the nifti header. epidewarp.fsl always
> assumes that the phase encode direction is in the row direction.
> doug
>
> On 11/13/2012 07:32 AM, Clark Fisher wrote:
> > Hi everyone,
> >
> > I recently switched the phase encoding direction of the functional
> sequence I've been using from F>>  H to  R>>  L  and ran into a problem
> with epidewarp.fsl (in version 4).  The unwarping was still happening along
> the F>>  H axis in the new images where phase encoding was R>>  L.
> >
> > (Note: I'm working with NHPs in sphinx position, but I'll describe my
> problem in standard coordinates to keep everything somewhat simpler)
> >
> > Because thought that epidewarp.fsl might be having a difficult time
> determining the phase encoding direction, I swapped the position of the F>>
>  H and R>>  L dimensions in my nifti file (going from LIP to IRP) and the
> dewarping now seems to work.
> >
> > Is there something going wrong in the unpacking such that the phase
> encoding information is lost?  Also, is the phase encoding information
> stored anywhere in the nifti, so that I can automatically detect and
> correct cases like this?
> >
> > Thanks for the help,
> > Clark
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] subdividing consistently within aparc.annot

[Satrajit Ghosh]

hi bruce,

sorry about the documentation snafu. i kept getting an error (having tried
--help, -h, -u and all the freesurfer variants) and in the end it turned
out i was operating out of a non-existent/stale directory and that's why i
wasn't getting any help!

this is very much what i needed.

cheers,

satra

On Sat, Oct 6, 2012 at 4:38 PM, Bruce Fischl wrote:

> Hi Satra
>
> isn't the code enough documentation enough?? You can use it in different
> ways. Try mris_divide_parcellation -help. You can either specify an area
> threshold and it will split annotations along their principle eigenaxis
> until they are under that (which may mean different number for different
> subjects), or you can give it a split file which explicitly tells it what
> to split (and it will do the same for each subject)
>
> cheers
> Bruce
> p.s.  mris_divide_parcellation -help
>
> mris_divide_parcellation [options] subject hemi sourceannot
> [splitfile|areathresh] outannot
>
>
> options
>   -help
>   -scalespecify offset scaling for rgb values (default=20)
>   -l   only process the label  (not implemented
> yet)
>
> This program divides one or more parcellations into divisions
> perpendicular to the long axis of the label.  The number of divisions
> can be specified in one of two ways, depending upon the nature of the
> fourth argument.
>
> First, a splitfile can be specified as the fourth argument. The
> splitfile is a text file with two columns. The first column is the
> name of the label in the source annotation, and the second column is
> the number of units that label should be divided into. The names of
> the labels depends upon the source parcellation.  For aparc.annot and
> aparc.a2005.annot, the names can be found in
> $FREESURFER_HOME/**FreeSurferColorLUT.txt.  For aparc.annot, the labels
> are between the ranges of 1000-1034.  For aparc.a2005s.annot, the
> labels are between the ranges of 1100-1181.  The name for the label is
> the name of the segmentation without the 'ctx-lh'. Note that the name
> included in the splitfile does not indicate the hemisphere. For
> example, 1023 is 'ctx-lh-posteriorcingulate'.  You should put
> 'posteriorcingulate' in the splitfile. Eg, to divide it into three
> segments, the following line should appear in the splitfile:
>
> posteriorcingulate 3
>
> Only labels that should be split need be specified in the splitfile.
>
> The second method is to specify an area threshold (in mm^2) as the
> fourth argument, in which case each label is divided until each
> subdivision is smaller than the area threshold.
>
> The output label name will be the original name with _divN appended,
> where N is the division number. N will go from 2 to the number of
> divisions. The first division has the same name as the original label.
>
>
> EXAMPLE:
>
> cd $SUBJECTS_DIR/mysubj001/label
>
> Create a split file to divide the superior frontal gyrus into 4
> segements and the precentral gyrus into 3 segments:
>
> echo superiorfrontal 4 >  splittable.txt
> echo precentral  3 >> splittable.txt
>
> Run program:
>
> mris_divide_parcellation mysubj001 rh aparc.annot splittable.txt
> rh.aparc.split-sfg+pc
>
> This reads in rh.aparc.annot, splits the SFG and PC, and and saves the
> result to rh.aparc.split-sfg+pc
>
> View
>
> tksurfer mysubj001 rh inflated -annot aparc.split-sfg+pc
>
> The SFG divisions will have the following names: superiorfrontal,
> superiorfrontal_div2, superiorfrontal_div3, superiorfrontal_div4. The
> PC divisions will be precentral, precentral_div2, precentral_div3.
>
>
>
>
>
>
> On Sat, 6 Oct 2012, Satrajit Ghosh wrote:
>
>  hi bruce,
>>   I'm not positive I understand what you want. Have you tried
>>   mris_divide_parcellation?
>>
>>
>> how do i use mris_divide_parcellation? any documentation somewhere?
>>
>> the basic idea is to create some form of voronoi tesselation of a region
>> constrained by a parameter n_sub_regions.
>>
>> subj1: aparc.annot -> e.g i want to break up stg into 6 regions
>> subj2: break up stg also into 6 regions such that there is a one to one
>> correspondence between the subj2 regions and subj1 regions.
>>
>> cheers,
>>
>> satra
>>
>>
>>
>>   Bruce
>>   On Wed, 3 Oct 2012, Satrajit Ghosh wrote:
>>
>> hi john,
>> thanks. that's the idea, but what i want is that
>> sub-division is done within
>> regions that are either determined automatically
>> through the freesurfer
>> classifi

Re: [Freesurfer] subdividing consistently within aparc.annot

[Satrajit Ghosh]

hi bruce,

I'm not positive I understand what you want. Have you tried
> mris_divide_parcellation?


how do i use mris_divide_parcellation? any documentation somewhere?

the basic idea is to create some form of voronoi tesselation of a region
constrained by a parameter n_sub_regions.

subj1: aparc.annot -> e.g i want to break up stg into 6 regions
subj2: break up stg also into 6 regions such that there is a one to one
correspondence between the subj2 regions and subj1 regions.

cheers,

satra


>
> Bruce
>
> On Wed, 3 Oct 2012, Satrajit Ghosh wrote:
>
>  hi john,
>> thanks. that's the idea, but what i want is that sub-division is done
>> within
>> regions that are either determined automatically through the freesurfer
>> classifier or through manual parcellations. not a fixed template of
>> parcels
>> that's transferred via the spherical registration.
>>
>> cheers,
>>
>> satra
>>
>>
>> On Wed, Oct 3, 2012 at 7:13 PM, John Griffiths <
>> j.davidgriffi...@gmail.com>
>> wrote:
>>
>>
>> Would the Lausanne2008 template from the connectome mapping toolkit
>> not do the trick?
>>
>> http://nipy.sourceforge.net/**nipype/users/examples/dmri_**
>> connectivity_advance<http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advance>
>> d.html
>>
>>
>>
>> On 3 October 2012 23:18, Satrajit Ghosh  wrote:
>>   hi bruce,
>> is there a way to divide consistently (same number of regions
>> and one to one correspondence - obviously not the exact same
>> areas) across subjects within aparc regions?
>>
>> cheers,
>>
>> satra
>>
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
>> The information in this e-mail is intended only for the person
>> to whom it is
>> addressed. If you believe this e-mail was sent to you in error
>> and the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>>  If the e-mail was sent
>> to you in error
>> but does not contain patient information, please contact the
>> sender and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>> --
>>
>> Mr. John Griffiths, MSc
>>
>> PhD Candidate
>>
>> Centre for Speech, Language, and the Brain
>>
>> Department of Experimental Psychology
>>
>> University of Cambridge, UK
>>
>>
>>
>>
>>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] subdividing consistently within aparc.annot

[Satrajit Ghosh]

hi john,

thanks. that's the idea, but what i want is that sub-division is done
within regions that are either determined automatically through the
freesurfer classifier or through manual parcellations. not a fixed template
of parcels that's transferred via the spherical registration.

cheers,

satra


On Wed, Oct 3, 2012 at 7:13 PM, John Griffiths
wrote:

>
>
> Would the Lausanne2008 template from the connectome mapping toolkit not do
> the trick?
>
>
> http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advanced.html
>
>
>
> On 3 October 2012 23:18, Satrajit Ghosh  wrote:
>
>> hi bruce,
>>
>> is there a way to divide consistently (same number of regions and one to
>> one correspondence - obviously not the exact same areas) across subjects
>> within aparc regions?
>>
>> cheers,
>>
>> satra
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
>
> Mr. John Griffiths, MSc
>
> PhD Candidate
>
> Centre for Speech, Language, and the Brain
>
> Department of Experimental Psychology
>
> University of Cambridge, UK
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] subdividing consistently within aparc.annot

[Satrajit Ghosh]

hi bruce,

is there a way to divide consistently (same number of regions and one to
one correspondence - obviously not the exact same areas) across subjects
within aparc regions?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] fswiki down?

[Satrajit Ghosh]

looks like the freesurfer wiki is down.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_surf2surf source and target annot formats

[Satrajit Ghosh]

hi doug,

thanks. we just wanted to verify that annot's are special. no need to hack
anything!

cheers,

satra

On Fri, May 25, 2012 at 11:27 AM, Douglas N Greve  wrote:

> Currently, yes. If this is a burden for you, I could hack something.
> There might be other ways such as converting the annot into a
> segmentation (mris_annotation2label), passing that to surf2surf with
> --sval (and --mapmethod nnf), then converting the output back to an
> annotation (mris_seg2annot). This is what happens internally.
> doug
>
>
>
> On 05/25/2012 09:52 AM, Satrajit Ghosh wrote:
> > hi doug,
> >
> > we are trying to figure out if for annot we *have to* use sval-annot
> > or if there is a way to do it with sval?
> >
> > cheers,
> >
> > satra
> >
> >
> > On Fri, May 25, 2012 at 9:46 AM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > If the source is an annot, then you need to use --sval-annot Is
> > this causing a problem?
> > doug
> >
> > On 5/24/12 6:48 PM, Arno Klein wrote:
> >>
> >> hello!
> >>
> >> in mri_surf2surf, does anyone know how to specify the source and
> >> target formats if --sval is annot without using --sval-annot, as
> >> in "--sfmt" or "--tfmt"?
> >>
> >> cheers,
> >> @rno
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu   Freesurfer@nmr.mgh.harvard.edu>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_surf2surf source and target annot formats

[Satrajit Ghosh]

hi doug,

we are trying to figure out if for annot we *have to* use sval-annot or if
there is a way to do it with sval?

cheers,

satra


On Fri, May 25, 2012 at 9:46 AM, Douglas Greve wrote:

>  If the source is an annot, then you need to use --sval-annot Is this
> causing a problem?
> doug
>
> On 5/24/12 6:48 PM, Arno Klein wrote:
>
>
>  hello!
>
>  in mri_surf2surf, does anyone know how to specify the source and target
> formats if --sval is annot without using --sval-annot, as in "--sfmt" or
> "--tfmt"?
>
>  cheers,
> @rno
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] request for dicom sequences on phantoms

[Satrajit Ghosh]

howdy brain imagers,

we are trying to put together a vocabulary of DICOM terms and their
definitions related to brain imaging. unfortunately, a lot of the useful
info is often in private tags and these differ from sequence to sequence
and from scanner to scanner.

to help us get at these tags, this is a shout out to folks to see if they
can make available a DICOM dataset (***without anonymizing***) collected
using their favorite current sequences on a phantom (no worries about
privacy - or so i hope). for time series/gradient direction sequences a
couple of volumes will do. we are interested in the DICOM header only not
the content of the images.

if you have such images or are willing to acquire them, please send me an
email *off the list* at: sa...@mit.edu and i will point you to an
appropriate location and method to upload your DICOM data.

cheers,

satra

ps. please do not reply all as you may not have post permissions on all the
lists.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_vol2surf failed, segmentation error

[Satrajit Ghosh]

hi Qingyang,

you can simply copy and paste the command line into the shell.

cheers,

satra


On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve
wrote:

> Can you run it outside of the pipeline to assure that it is not a
> pipeline issue?
> doug
>
> On 03/18/2012 08:54 AM, Qingyang Li wrote:
> > Hi all,
> > I am new to the freesurfer world.
> > I was running a pipeline where I met an error. Here is the command I
> > run and the error message:
> >
> > Command:
> > mri_vol2surf --hemi lh --noreshape --o
> >
> /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz
> > --reg
> >
> /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat
> > --projfrac 0.500 --mov
> >
> /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz
> > Standard output:
> > srcvol =
> >
> /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz
> > srcreg =
> >
> /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = lh
> > ProjFrac = 0.5
> > thickness = thickness
> > reshape = 0
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > INFO: changing type to float
> > Done loading volume
> > Reading surface /NKI_recon_subjects/sub/surf/lh.white
> > Done reading source surface
> > Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness
> > Done
> > Mapping Source Volume onto Source Subject Surface
> >  1 0.5 0.5 0.5
> > using old
> > Done mapping volume to surface
> > Standard error:
> > Segmentation fault
> > Return code: 139
> > Interface SampleToSurface failed to run.
> >
> >
> > Thank you all in advance!
> >
> > Yang
> >
> > --
> > Qingyang Li
> >
> > Balance and focus.
> >
> >
> > On Sun, Mar 18, 2012 at 8:28 AM,
> >  > > wrote:
> >
> > Mailing list subscription confirmation notice for mailing list
> > Freesurfer
> >
> > We have received a request from 67.244.70.75 for subscription of your
> > email address, "con...@gmail.com ", to the
> > freesurfer@nmr.mgh.harvard.edu
> >  mailing list.  To confirm
> > that you want
> > to be added to this mailing list, simply reply to this message,
> > keeping the Subject: header intact.  Or visit this web page:
> >
> >
> https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbcee3ff0f76888c79e7704b4a03a
> >
> >
> > Or include the following line -- and only the following line -- in a
> > message to freesurfer-requ...@nmr.mgh.harvard.edu
> > :
> >
> >confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a
> >
> > Note that simply sending a `reply' to this message should work from
> > most mail readers, since that usually leaves the Subject: line in the
> > right form (additional "Re:" text in the Subject: is okay).
> >
> > If you do not wish to be subscribed to this list, please simply
> > disregard this message.  If you think you are being maliciously
> > subscribed to the list, or have any other questions, send them to
> > freesurfer-ow...@nmr.mgh.harvard.edu
> > .
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you b

Re: [Freesurfer] [BUG] epidewarp.fsl

[Satrajit Ghosh]

hi doug,

here is the error, it told me there was a problem in an if statement
somewhere.

if you use smooth = 2.0 instead of 2 you will get the error.

cheers,

satra

---
[snip]
fslmerge -t /mindhive/gablab/users/keshavan/scripts/BrainImagingPipeline
s/utils/test/fmunwarp/temp/ph.nii.gz /mindhive/gablab/users/keshava
n/scripts/BrainImagingPipelines/utils/test/fmunwarp/temp/ph.zeros.nii.gz
/mindhive/gablab/users/keshavan/scripts/BrainImagingPipelines/utils/test/fm
unwarp/temp/dph
Masking with /mindhive/gablab/users/keshavan/scripts/BrainImagingPipeline
s/utils/test/fmunwarp/temp/brain.nii.gz
Standard error:
if: Badly formed number.
Return code: 1
Interface EPIDeWarp failed to run.
---

On Mon, Mar 26, 2012 at 10:39 AM, Douglas N Greve  wrote:

> what does it do? What is the terminal output?
>
> Satrajit Ghosh wrote:
>
>> epidewarp.fsl does not take non-integer smoothing kernel sizes.
>>
>> cheers,
>>
>> satra
>>
>> --**--**
>> 
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: 
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>  If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] [BUG] epidewarp.fsl

[Satrajit Ghosh]

epidewarp.fsl does not take non-integer smoothing kernel sizes.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [freesurfer] Is there any way to get the image from Tksurfer with white background?

[Satrajit Ghosh]

depending on what you are doing you could use PySurfer.

cheers,

satra

On Mon, Mar 12, 2012 at 6:04 PM, Bruce Fischl wrote:

> no, sorry
> On Mon, 12 Mar 2012, zhang mingxia wrote:
>
>  Hi dear freesurfer experts,
>> I am making pictures for publication. The images saving from Tksurfer
>> are black backgrounds. Is there any way to save the image with white
>> background?
>>
>> Thank you very much
>>
>> Mingxia Zhang
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Use bbregister parameters to transform to EPI geometry

[Satrajit Ghosh]

ah in that case you need to multiply the affine stored in one session's
bbreg with the inverse of the other bbreg from the target session and then
use mri_vol2vol with the composite transform. note: only nearest or
trilinear interp

cheers,

satra


On Tue, Dec 20, 2011 at 12:07 AM, Michael Waskom wrote:

> OK, cool, I'll look into this for the future.
>
> But back to my original question. If I already have data preprocessed with
> several runs, each run motion-corrected within-session, and an affine
> registration from each run's space to the anatomical determined by
> bbregister, is there any way to use those transformation parameters to take
> the function scans into a common space that retains the original voxel size?
>
> Michael
>
>
> On Mon, Dec 19, 2011 at 1:34 PM, Satrajit Ghosh  wrote:
>
>> hi michael,
>>
>> so for each frame of every session you get a bbreg file and the script
>> ends up aligning the volumes to some reference. all you need to do is
>> propagate that reference across your sessions. you might for example want
>> this to be the middle volume of your entire experiment.
>>
>> cheers,
>>
>> satra
>>
>>
>> On Mon, Dec 19, 2011 at 10:18 PM, Michael Waskom wrote:
>>
>>> Sorry, I guess it's not clear what I'm hoping to do.
>>>
>>> Because I'm going to use this data for mvpa, I don't want to resample
>>> into 1x1x1 voxels or go onto the surface. But I have multiple runs that I
>>> want to use, so I need there to be a voxel-to-brain correspondence across
>>> the different runs.
>>>
>>> Michael
>>>
>>>
>>> On Mon, Dec 19, 2011 at 12:46 PM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>
>>>> It will output a register.dat for each frame. You can extract the frame
>>>> from the time series (mri_convert --frame ), apply the reg with mri_vol2vol
>>>> or mri_vol2surf, then concatenate the results back into a time series
>>>> (mri_concat)
>>>> doug
>>>>
>>>> Michael Waskom wrote:
>>>>
>>>>> Hi Satra and Doug,
>>>>>
>>>>> That script is good to know about.  But, from what I can tell, it
>>>>> looks like it will output a timeseries in the same space as the original
>>>>> template (each frame gets transformed with a combination of the matrix
>>>>> specifying its registration to the anatomical and the inverse of the 
>>>>> matrix
>>>>> specifying the registration from the template to the anatomical). So this
>>>>> might give me somewhat better motion correction, but it won't give me a
>>>>> common space across runs.
>>>>>
>>>>> Best,
>>>>> Michael
>>>>>
>>>>> On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve <
>>>>> gr...@nmr.mgh.harvard.edu 
>>>>> <mailto:gr...@nmr.mgh.harvard.**edu>>
>>>>> wrote:
>>>>>
>>>>>That may or may not do what you want. I think that version keeps the
>>>>>functional data in the functional space. It would be better to
>>>>>register
>>>>>each TR to the anat, then simply sample each TR to the anatomical
>>>>>space
>>>>>(volume or surface) rather than going back into functional space.
>>>>>doug
>>>>>
>>>>>
>>>>>Satrajit Ghosh wrote:
>>>>>> hey mike,
>>>>>>
>>>>>> take a look at:
>>>>>>
>>>>>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>>>>> greve/mc-bbr<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr>
>>>>>>
>>>>>> cheers,
>>>>>>
>>>>>> satra
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom
>>>>>mailto:mwas...@stanford.edu>
>>>>>> <mailto:mwas...@stanford.edu <mailto:mwas...@stanford.edu>>**>
>>>>> wrote:
>>>>>>
>>>>>> Hi Doug,
>>>>>>
>>>>>> Is it possible to use the bbregister parameters to resample a
>>>>>> functional image such that it is in register with th

Re: [Freesurfer] Use bbregister parameters to transform to EPI geometry

[Satrajit Ghosh]

hi michael,

so for each frame of every session you get a bbreg file and the script ends
up aligning the volumes to some reference. all you need to do is propagate
that reference across your sessions. you might for example want this to be
the middle volume of your entire experiment.

cheers,

satra

On Mon, Dec 19, 2011 at 10:18 PM, Michael Waskom wrote:

> Sorry, I guess it's not clear what I'm hoping to do.
>
> Because I'm going to use this data for mvpa, I don't want to resample into
> 1x1x1 voxels or go onto the surface. But I have multiple runs that I want
> to use, so I need there to be a voxel-to-brain correspondence across the
> different runs.
>
> Michael
>
>
> On Mon, Dec 19, 2011 at 12:46 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> It will output a register.dat for each frame. You can extract the frame
>> from the time series (mri_convert --frame ), apply the reg with mri_vol2vol
>> or mri_vol2surf, then concatenate the results back into a time series
>> (mri_concat)
>> doug
>>
>> Michael Waskom wrote:
>>
>>> Hi Satra and Doug,
>>>
>>> That script is good to know about.  But, from what I can tell, it looks
>>> like it will output a timeseries in the same space as the original template
>>> (each frame gets transformed with a combination of the matrix specifying
>>> its registration to the anatomical and the inverse of the matrix specifying
>>> the registration from the template to the anatomical). So this might give
>>> me somewhat better motion correction, but it won't give me a common space
>>> across runs.
>>>
>>> Best,
>>> Michael
>>>
>>> On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu 
>>> <mailto:gr...@nmr.mgh.harvard.**edu>>
>>> wrote:
>>>
>>>That may or may not do what you want. I think that version keeps the
>>>functional data in the functional space. It would be better to
>>>register
>>>each TR to the anat, then simply sample each TR to the anatomical
>>>space
>>>(volume or surface) rather than going back into functional space.
>>>doug
>>>
>>>
>>>Satrajit Ghosh wrote:
>>>> hey mike,
>>>>
>>>> take a look at:
>>>>
>>>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>>> greve/mc-bbr<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr>
>>>>
>>>> cheers,
>>>>
>>>> satra
>>>>
>>>>
>>>>
>>>> On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom
>>>mailto:mwas...@stanford.edu>
>>>> <mailto:mwas...@stanford.edu <mailto:mwas...@stanford.edu>>**>
>>> wrote:
>>>>
>>>> Hi Doug,
>>>>
>>>> Is it possible to use the bbregister parameters to resample a
>>>> functional image such that it is in register with the anatomical
>>>> image but retains the epi geometry? I actually don't care so
>>>much
>>>> about the epi-anat registration, but what I would like to be
>>>able
>>>> to do is motion correct and otherwise preprocess my timeserieses
>>>> within session* and then move different sessions into a common
>>>> volumetric space for analysis. As I have great faith in
>>>> bbregister, ideally the transformation would be determined with
>>>> this method (I suspect it is superior to picking a slice
>>>from one
>>>> of the sessions to use as a motion correction target across all
>>>> sessions). Additionally, I would prefer not to upsample the
>>>source
>>>> voxels either into 1x1x1 anatomical geometry or to surface
>>>> vertices. Unfortunately, my affine understanding isn't deep
>>>enough
>>>> for me to figure this out myself.
>>>>
>>>> Does that make sense, and (if so) do you have any ideas?
>>>>
>>>> Thanks!
>>>> Michael
>>>>
>>>> * Here i use "session" in the sense of "run", which is
>>>different I
>>>> think from FSFast terminology so apologies for any confusion.
>>&

Re: [Freesurfer] Use bbregister parameters to transform to EPI geometry

[Satrajit Ghosh]

hey mike,

take a look at:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr

cheers,

satra



On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom wrote:

> Hi Doug,
>
> Is it possible to use the bbregister parameters to resample a functional
> image such that it is in register with the anatomical image but retains the
> epi geometry? I actually don't care so much about the epi-anat
> registration, but what I would like to be able to do is motion correct and
> otherwise preprocess my timeserieses within session* and then move
> different sessions into a common volumetric space for analysis. As I have
> great faith in bbregister, ideally the transformation would be determined
> with this method (I suspect it is superior to picking a slice from one of
> the sessions to use as a motion correction target across all sessions).
> Additionally, I would prefer not to upsample the source voxels either into
> 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine
> understanding isn't deep enough for me to figure this out myself.
>
> Does that make sense, and (if so) do you have any ideas?
>
> Thanks!
> Michael
>
> * Here i use "session" in the sense of "run", which is different I think
> from FSFast terminology so apologies for any confusion.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] surfaces and gifti

[Satrajit Ghosh]

hi all,

this command: mris_convert --combinesurfs lh.pial rh.pial pial.gii.gz

resulted in lh.pial.gii.gz (the help says it should generate pial.gii.gz).

a related question. once i have this gifti file how do i get
annotations+curvature info also into the file? (the gifti schema supports
this right?)

essentially i am looking for a way to bundle the surface information into a
single gifti container.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Satrajit Ghosh]

hi nick,

i really like pedro's idea of tracking through instance tracking as opposed
to licenses. on a separate project we are setting up the ability to pull up
as many instances as necessary and install whatever software environment
that's needed to run your analysis. we'll try to ensure that each person
has a license file in their "folder" that we can pull.

however given the current licensing of freesurfer, one can easily remove
the license components. that's why i feel the instance tracking is painless
and provides you with a better estimate of the number of times freesurfer
is run. as an example, at mit we have a single license which everybody uses
and that's not a great way for you to track the number of projects or
subjects run through freesurfer.

cheers,

satra

2011/11/18 Nick Schmansky 

> Long term, after we put together an 'official' instance of the AMI with
> scripts (which might well be an instance that Pedro Paulo created) I
> think sftp'ing the .license file to each instance is the way to go.
> The .license file need only apply to the user (not each instance or
> run).
>
> N.
>
> On Fri, 2011-11-18 at 08:00 -0800, Joshua Lee wrote:
> > When I used the AMI, (maybe not Pedro's), so I sftp'd a license file
> > to each instance prior to running an analysis. Not a big deal. I
> > didn't get a new license for each instance, but copied the same one to
> > multiple instances.
> >
> > Joshua
> >
> > 2011/11/18 Pedro Paulo de Magalhães Oliveira Junior
> > 
> > I have restored the image: 060244368407/FREESURFER51
> >
> >
> > I'll create a web service that can log the number of instances
> > spawned. Is that ok with you?
> >
> -
> > Pedro Paulo de Magalhães Oliveira Junior
> > Netfilter & SpeedComm Telecom
> > -- www.netfilter.com.br
> > -- For
> > mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
> >
> >
> >
> >
> >
> >
> >
> > 2011/11/18 Bruce Fischl 
> > Hi PPJ,
> >
> > I would rather people use FS without licenses than
> > find themselves unable to use it, so why not leave it
> > for now. Can you put a request that they first
> > download a license or register on your website?
> > Alternatively, can you just remove the .license file
> > from the AMI forcing the users to get one?
> >
> > thanks for making this available
> > Bruce
> >
> >
> >
> > On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira
> > Junior wrote:
> >
> >
> > As requested I removed the AMI image because
> > that image contains a .license file.
> > I can republish the image when we find a
> > solution for the licensing issue.
> >
> >
> -
> > Pedro Paulo de Magalhães Oliveira Junior
> >
> > Netfilter & SpeedComm Telecom--
> > www.netfilter.com.br
> >
> > -- For
> > mobile:
> http://itunes.apple.com/br/artist/netfilter/id365306441
> >
> >
> >
> >
> > 2011/11/15 Joshua Lee 
> >  It would be great if Freesurfer
> > maintained an official AMI. One important
> > reason to do so is security. If the
> >  AMI is maintained by the organization,
> > then people can feel reassured that their data
> > is not being downloaded to
> >  a compromised instance, not that any on
> > this board would have such malicious intent.
> > Moreover, it could contain
> >  such scripts as makes the analysis
> > process easier.
> >
> >  -
> > Joshua Lee
> > Graduate Student
> > Center for Mind and Brain &
> > Department of Psychology
> > University of California, Davis
> > 530.747.3805
> >
> >
> > 2011/11/14 Pedro Paulo de Magalhães Oliveira
> > Junior 
> >  Ok. I'll label as private this AMI that
> > has .license file.
> > Maybe we can make a tutorial on how to create
> > an AMI instead.
> >
> -
> > Pedro Paulo de Magalhães Oliveira Junior
> >
> >

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Satrajit Ghosh]

hi nolan,

i think starcluster is a great way to create a cluster on aws. but for
those wanting to create a single instance and install things on an ami
without actually having a large ami, fabric might be a good option.

fabric:
http://docs.fabfile.org/en/1.3.2/index.html

example: (another neurodebian ami)
https://github.com/wholeslide/ipython_in_a_box/blob/master/fabfile.py

cheers,

satra

On Sat, Nov 12, 2011 at 6:11 AM, Nolan Nichols  wrote:

> Thanks, Pedro!
>
> I am glad to see that you posted a public AMI for freesurfer. And
> thanks to Thomas for producin documentation on how to use it.
>
> This thread inspired me share a StarCluster AMI (ami-27f1384e in the
> us-east-1 region) that I built for batch FS jobs, which includes the
> initial setup for installing tools from the NeuroDebian repository.
> I've also been playing around with using s3fs, which allows Amazon's
> S3 to be mounted as a drive and accessed directly as the
> "subjects_dir".
>
> The AMI can be launched here:
>
> https://console.aws.amazon.com/ec2/home?region=us-east-1#launchAmi=ami-27f1384e
>
> I did not include the .license for FS as I wasn't sure about licensing
> issues, but I would be happy to publish an AMI with a built-in license
> if I get the go ahead. For now you will need to start a cluster and
> your license to each instance.
>
> A few details:
>
> Ubuntu 10.04 x86
> built from StarClusters ami-8cf913e5
> us-east-1 region
> See the StarCluster details at http://web.mit.edu/stardev/cluster/
> Customizing StarCluster
> (http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html
> )
> s3fs (http://code.google.com/p/s3fs/)
> Freesurfer 5.1 32-bit
> NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, etc.)
>
> Thanks again for starting this thread, and let me know if I can help
> in any way. It would be great to see "cloud" resources be readily
> accessibly to the community with minimal effort to get a cluster with
> freesurfer and tools available via neurodebian up and running.
>
> Cheers,
>
> Nolan
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Satrajit Ghosh]

hi pedro,

will this work with gpu instances as well?

cheers,

satra

2011/11/9 Pedro Paulo de Magalhães Oliveira Junior 

> Some weeks ago I was asked about a public image (AMI) to run in the Amazon
> EC2 infrastructure
>
> If you want to use FreeSurfer in the EC2 infrastructure you can use this
> public AMI: *060244368407/FREESURFER51*
>
> Just for your information this AMI can run a recon-all in 23 hours in an
> Amazon AWS Small Instance. So with the current Amazon cost per Small
> Instance/Hour you'll have a recon-all for USD 2.04
>
> Amazon request a credit card in order to create an account in
> http://aws.amazon.com
>
> Hope it helps,
>
> Pedro Paulo Jr.
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] graph of region neighborhood

[Satrajit Ghosh]

hi folks,

do you happen to have any tool/script that produces a graph of aparc region
neighborhood? with perhaps the edge weight being the length of shared
boundary.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] strange freeview issue

[Satrajit Ghosh]

just completing this thread. our sysadmin found a solution that works well
for us:

you can see glxgears working in NX if you type:
export LIBGL_ALWAYS_INDIRECT=yes
in the terminal before running glxgears. it's not fast, but it works. i
think the same holds true for VNC.
-matt


cheers,

satra


On Tue, Sep 27, 2011 at 8:40 PM, Satrajit Ghosh  wrote:

> hi,
>
> we are seeing a strange freeview issue at mit and just wanted to check if
> anybody else has seen this. we are running natty narwhal (ubuntu 11.04).
>
> details here:
>
> https://github.com/gablab/mindhive/issues/1
>
> cheers,
>
> satra
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] strange freeview issue

[Satrajit Ghosh]

thanks nick.

tried with 5.1.0 same issue. here is the output from glxgears.

$ glxgears
Error: couldn't get an RGB, Double-buffered visual

i am beginning to suspect it as a driver issue.

cheers,

satra


On Wed, Sep 28, 2011 at 11:17 AM, Nick Schmansky
wrote:

> i'm able to replicate what you see on my mac (leopard, w/ XQuartz)
> connecting via ssh -Y to a linux machine and running fs v5.0.0.
> however, freeview works in this setup using fs 5.1.0.  the change
> between version is that freeview now uses Qt (instead of Wx).  can you
> switch to v5.1.0?  or copy the freeview from 5.1.0 to your 5.0.0
> installation?  you would need to copy:
>
> freesurfer/lib/qt
> freesurfer/bin/freeview
> freesurfer/bin/freeview.bin
> freesurver/bin/qt_setup.csh
>
> n.
>
>
>
> On Tue, 2011-09-27 at 20:40 -0400, Satrajit Ghosh wrote:
> > hi,
> >
> >
> > we are seeing a strange freeview issue at mit and just wanted to check
> > if anybody else has seen this. we are running natty narwhal (ubuntu
> > 11.04).
> >
> >
> > details here:
> >
> >
> > https://github.com/gablab/mindhive/issues/1
> >
> >
> > cheers,
> >
> > satra
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] strange freeview issue

[Satrajit Ghosh]

hi,

we are seeing a strange freeview issue at mit and just wanted to check if
anybody else has seen this. we are running natty narwhal (ubuntu 11.04).

details here:

https://github.com/gablab/mindhive/issues/1

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] .img extension read as analyze even though hdr says nifti1

[Satrajit Ghosh]

hi all,

when a .img extension file is passed to freesurfer routines, it is read in
as analyze even if the header says it's a nifti image. we have observed that
this causes a left-right flip in some cases. since a .img cannot exist
without a header to be meaningful, shouldn't the appropriate type be
detected from the header?

also it would be good to know if this behavior is consistent across all of
freesurfer or restricted to certain binaries.

see below for mri_info output

cheers,

satra

$ mri_info con_0001.img
Volume information for con_0001.img
  type: analyze4d
dimensions: 79 x 95 x 68
   voxel sizes: 2., 2., 2.
  type: FLOAT (3)
   fov: 79.000
   dof: 0
xstart: -39.5, xend: 39.5
ystart: -47.5, yend: 47.5
zstart: -34.0, zend: 34.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
-1.
  : x_a =   0., y_a =   1., z_a =   0., c_a =
-17.
  : x_s =   0., y_s =   0., z_s =   1., c_s =
18.
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -2.   0.   0.78.
0.   2.   0.  -112.
0.   0.   2.   -50.
0.   0.   0. 1.

voxel-to-ras determinant -8

ras to voxel transform:
   -0.5000   0.   0.39.
   -0.   0.5000  -0.56.
   -0.  -0.   0.500025.
0.   0.   0. 1.

$ mri_info con_0001.hdr
Volume information for con_0001.hdr
  type: nifti1
dimensions: 79 x 95 x 68
   voxel sizes: 2., 2., 2.
  type: FLOAT (3)
   fov: 79.000
   dof: 0
xstart: -39.5, xend: 39.5
ystart: -47.5, yend: 47.5
zstart: -34.0, zend: 34.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
-1.
  : x_a =   0., y_a =   1., z_a =   0., c_a =
-17.
  : x_s =   0., y_s =   0., z_s =   1., c_s =
18.
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -2.   0.   0.78.
0.   2.   0.  -112.
0.   0.   2.   -50.
0.   0.   0. 1.

voxel-to-ras determinant -8

ras to voxel transform:
   -0.5000   0.   0.39.
   -0.   0.5000  -0.56.
   -0.  -0.   0.500025.
0.   0.   0. 1.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] PySurfer - A package for visualizing surfaces

[Satrajit Ghosh]

hi mike,

In theory it could, as we use Nibabel for i/o and they support Gifti.
> However, I have no data in Gifti format at the moment to work with, so
> at the moment I would say we are Freesurfer specific.
>

freesurfer does support giftis.

mris_convert --combinesurfs fsaverage/surf/lh.inflated
fsaverage/surf/rh.inflated test.gii

mris_convert fsaverage/surf/lh.inflated ./lh.test2.gii

would be awesome to be able to have gifti support and direct nifti overlay
with a bbreg.dat registration or identity instead of having to create an
overlay file.

cheers,

satra


>
> Best,
> Michael
>
> On Fri, Jul 22, 2011 at 2:09 PM, Matt Glasser  wrote:
> > Hi Michael,
> >
> > Out of curiosity, does this also support the GIFTI format?  If so, one
> could
> > use it to view surface data from a wide variety of software packages.
> >
> > Thanks,
> >
> > Matt.
> >
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael
> Waskom
> > Sent: Friday, July 22, 2011 1:07 PM
> > To: Freesurfer@nmr.mgh.harvard.edu
> > Cc: Alexandre Gramfort; Scott Burns
> > Subject: [Freesurfer] PySurfer - A package for visualizing surfaces
> >
> > Dear Freesurfers,
> >
> > We are pleased to announce the 0.1 release of PySurfer, a Python-based
> > package for the visualization of surface data from Freesurfer.  Please
> > see our website at http://pysurfer.github.com/ for information on how
> > to install the package and a gallery of examples.  We hope you'll find
> > it useful in your research!
> >
> > Best,
> > Michael Waskom
> > Alexandre Gramfort
> > Scott Burns
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom it
> is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> >
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] re-running recon-all failing

[Satrajit Ghosh]

update: node on cluster had failing memory chip!

cheers,

satra


On Mon, Jul 18, 2011 at 4:16 PM, Satrajit Ghosh  wrote:

> hi all,
>
> i'm trying to rerun some subjects processed with 5.0 with 5.1 and am
> getting the following error on all the subjects.
>
> simply executing recon-all -s subjid -all
>
> any ideas?
>
> cheers,
>
> satra
>
>
> -- unfolding failed - restoring original position
> 
> 0750: dt=0.001250, rms=0.380 (0.000%), neg=0, invalid=766
> writing output transformation to transforms/talairach.m3z...
> GCAMwrite
> GCAMwrite:: m3z loop
> GCAMwrite:: the command is:  gzip -f -c > transforms/talairach.m3z
> registration took 4 hours, 1 minutes and 50 seconds.
> ERROR: mri_ca_register with non-zero status 1
> but continuing despite the error
> #--
> #@# CA Reg Inv Mon Jul 18 14:54:53 EDT 2011
> /g2/users/satra/TESTCVS/surfaces/ek041bk/mri
>
>  mri_ca_register -invert-and-save transforms/talairach.m3z
>
> Loading, Inverting, Saving, Exiting ...
> Reading transforms/talairach.m3z
> zcat transforms/talairach.m3z
> Inverting GCAM
> Saving inverse
> ERROR: mri_ca_register with non-zero status 0
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] re-running recon-all failing

[Satrajit Ghosh]

hi all,

i'm trying to rerun some subjects processed with 5.0 with 5.1 and am getting
the following error on all the subjects.

simply executing recon-all -s subjid -all

any ideas?

cheers,

satra


-- unfolding failed - restoring original position

0750: dt=0.001250, rms=0.380 (0.000%), neg=0, invalid=766
writing output transformation to transforms/talairach.m3z...
GCAMwrite
GCAMwrite:: m3z loop
GCAMwrite:: the command is:  gzip -f -c > transforms/talairach.m3z
registration took 4 hours, 1 minutes and 50 seconds.
ERROR: mri_ca_register with non-zero status 1
but continuing despite the error
#--
#@# CA Reg Inv Mon Jul 18 14:54:53 EDT 2011
/g2/users/satra/TESTCVS/surfaces/ek041bk/mri

 mri_ca_register -invert-and-save transforms/talairach.m3z

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
zcat transforms/talairach.m3z
Inverting GCAM
Saving inverse
ERROR: mri_ca_register with non-zero status 0
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Request for DICOMS

[Satrajit Ghosh]

hi,

if you have pointers to publicly available DICOM data or willing to share
such data publicly from different scanners and acquisition sequences for
structural, diffusion and functional data from human participants, please
contact me off list.

currently, the more varied the scanners and sequences, the better. i'm not
looking for full datasets here, but primarily the ability to mine the
various tags and metadata that exist across common image acquisitions.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] recon-all parallel execution of hemi stages

[Satrajit Ghosh]

it seems we could run lh/rh processing stages of recon-all in parallel.
however, i think they will write to the same log files. is there a way to
specify a different log-file prefix?

are there any other common files that these hemisphere based operations
write to? concurrent reading i'm assuming is ok.

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mri_convert dicom conversion

[Satrajit Ghosh]

hi,

mri_convert TrioTim/123456-10-1.dcm test.nii.gz

will scan all files in the dicom directory to get at series 10. in the above
scenario, i know that the files corresponding to the run are
123456-10-*.dcm. is there a way to leverage this information, so that it
does not scan the entire directory?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] brainmask

[Satrajit Ghosh]

if one wants to get at the brain only (similar to bet), is brainmask.mgz the
best file to use? on some of our data, we are noticing a lot of eyeball.

i presume one can use aseg as an alternative. is this more recommended than
brainmask.mgz? also, is the total brain volume computation based on aseg or
some other file?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_convert resample

[Satrajit Ghosh]

can i use mri_convert to resample a 4-d nifti volume? currently it appears
to write out just one frame.

cmdline used:

mri_convert -vs 2 2 2 r234000-20-1_warped.nii
r234000-20-1_warped_fsresample.nii

the input volume has 51 timepoints the output vol has 1.

would you recommend another, more appropriate function?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Bvecs and image orientation

[Satrajit Ghosh]

This question was asked on the FSL list and I thought it would be pertinent
on this list as well in relation to mri_convert.

-- Forwarded message --
From: Saad Jbabdi 

The bvecs are supposed to be relative to the image grid.

On 22 Sep 2009, at 13:34, Laura Mancini wrote:

 Dear all,
>
> In FSL, do the x, y, z components of the bvecs correspond to the image
> axes (i.e. along the directions of the data matrix indices), or to the
> patient axes as defined in the nifti header, or something else?
>
> Many thanks,
> Laura
>


when one converts a dicom data set containing diffusion data with
mri_convert it generates bvecs and bvals. the bvecs are unit vectors
relative to some coordinate system. is this the coordinate system of the
scanner or the coordinate system of the image volume?

cheers,

satra
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer